Multiple sequence alignment - TraesCS2B01G324500

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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 TraesCS2B01G324500 chr2B 100.000 7245 0 0 1 7245 463854416 463861660 0.000000e+00 13380.0
1 TraesCS2B01G324500 chr2B 94.786 4526 166 40 1888 6372 464021494 464025990 0.000000e+00 6986.0
2 TraesCS2B01G324500 chr2B 90.585 2719 153 37 4100 6785 463769013 463771661 0.000000e+00 3507.0
3 TraesCS2B01G324500 chr2B 90.854 2460 147 42 1704 4101 463766520 463768963 0.000000e+00 3225.0
4 TraesCS2B01G324500 chr2B 88.521 1028 61 25 883 1887 464020320 464021313 0.000000e+00 1192.0
5 TraesCS2B01G324500 chr2B 82.138 767 62 36 884 1611 463765712 463766442 8.100000e-164 588.0
6 TraesCS2B01G324500 chr2B 90.728 151 13 1 714 864 775849120 775848971 4.430000e-47 200.0
7 TraesCS2B01G324500 chr2B 95.238 42 2 0 6811 6852 463771740 463771781 4.690000e-07 67.6
8 TraesCS2B01G324500 chr2A 93.963 4903 197 50 1524 6372 529792298 529797155 0.000000e+00 7323.0
9 TraesCS2B01G324500 chr2A 95.807 4531 107 21 1704 6192 529692201 529696690 0.000000e+00 7238.0
10 TraesCS2B01G324500 chr2A 90.532 2461 154 42 1704 4101 528906129 528908573 0.000000e+00 3181.0
11 TraesCS2B01G324500 chr2A 93.067 2106 108 18 4100 6185 528908623 528910710 0.000000e+00 3046.0
12 TraesCS2B01G324500 chr2A 95.111 900 40 3 6224 7122 529696687 529697583 0.000000e+00 1415.0
13 TraesCS2B01G324500 chr2A 90.081 988 53 20 714 1687 529691199 529692155 0.000000e+00 1240.0
14 TraesCS2B01G324500 chr2A 94.050 605 28 5 861 1459 529791497 529792099 0.000000e+00 911.0
15 TraesCS2B01G324500 chr2A 88.762 525 43 7 6269 6784 528910737 528911254 4.770000e-176 628.0
16 TraesCS2B01G324500 chr2A 81.258 779 58 37 884 1611 528905302 528906043 3.820000e-152 549.0
17 TraesCS2B01G324500 chr2A 89.189 148 13 3 719 865 729580015 729579870 1.610000e-41 182.0
18 TraesCS2B01G324500 chr2A 88.889 108 6 5 1582 1687 529792118 529792221 2.120000e-25 128.0
19 TraesCS2B01G324500 chr2A 84.028 144 7 2 7118 7245 529700140 529700283 2.740000e-24 124.0
20 TraesCS2B01G324500 chr2D 94.036 4678 192 39 1757 6393 392052534 392057165 0.000000e+00 7012.0
21 TraesCS2B01G324500 chr2D 90.614 2461 151 43 1704 4101 391850723 391853166 0.000000e+00 3192.0
22 TraesCS2B01G324500 chr2D 91.881 2217 112 19 4100 6297 391853216 391855383 0.000000e+00 3035.0
23 TraesCS2B01G324500 chr2D 94.879 742 36 2 714 1454 392051610 392052350 0.000000e+00 1158.0
24 TraesCS2B01G324500 chr2D 80.940 766 72 34 884 1611 391849912 391850641 8.270000e-149 538.0
25 TraesCS2B01G324500 chr2D 90.000 400 36 3 6393 6792 391863153 391863548 1.390000e-141 514.0
26 TraesCS2B01G324500 chr2D 92.265 181 10 3 1507 1687 392052353 392052529 3.350000e-63 254.0
27 TraesCS2B01G324500 chr2D 100.000 36 0 0 6817 6852 391863605 391863640 4.690000e-07 67.6
28 TraesCS2B01G324500 chr5B 94.930 710 36 0 1 710 490542103 490541394 0.000000e+00 1112.0
29 TraesCS2B01G324500 chr5B 94.507 710 39 0 1 710 644506126 644505417 0.000000e+00 1096.0
30 TraesCS2B01G324500 chr5B 86.667 75 10 0 2230 2304 62958504 62958578 4.660000e-12 84.2
31 TraesCS2B01G324500 chr6B 94.789 710 37 0 1 710 11732402 11731693 0.000000e+00 1107.0
32 TraesCS2B01G324500 chr6B 73.614 523 106 22 4237 4755 227096126 227096620 9.660000e-39 172.0
33 TraesCS2B01G324500 chr3B 94.789 710 37 0 1 710 582414162 582413453 0.000000e+00 1107.0
34 TraesCS2B01G324500 chr3B 94.366 710 40 0 1 710 449312553 449311844 0.000000e+00 1090.0
35 TraesCS2B01G324500 chr3B 90.000 150 13 2 714 863 722304891 722304744 7.420000e-45 193.0
36 TraesCS2B01G324500 chr3B 88.667 150 16 1 714 863 722349285 722349137 1.610000e-41 182.0
37 TraesCS2B01G324500 chr3B 85.870 92 11 2 7088 7177 98140949 98141040 5.980000e-16 97.1
38 TraesCS2B01G324500 chr1B 94.789 710 37 0 1 710 119486504 119485795 0.000000e+00 1107.0
39 TraesCS2B01G324500 chr1B 94.789 710 37 0 1 710 306976735 306977444 0.000000e+00 1107.0
40 TraesCS2B01G324500 chr7B 94.507 710 39 0 1 710 703145450 703144741 0.000000e+00 1096.0
41 TraesCS2B01G324500 chr4B 94.366 710 40 0 1 710 627251665 627250956 0.000000e+00 1090.0
42 TraesCS2B01G324500 chr4A 90.845 142 12 1 714 855 445811994 445812134 9.600000e-44 189.0
43 TraesCS2B01G324500 chr6D 73.321 521 112 18 4237 4755 128257908 128258403 4.500000e-37 167.0
44 TraesCS2B01G324500 chr4D 91.463 82 5 2 778 859 58386660 58386739 2.140000e-20 111.0
45 TraesCS2B01G324500 chr5A 88.889 81 6 3 768 846 531897753 531897674 5.980000e-16 97.1
46 TraesCS2B01G324500 chr1D 83.696 92 13 1 7088 7177 210572216 210572307 1.300000e-12 86.1


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 TraesCS2B01G324500 chr2B 463854416 463861660 7244 False 13380.000000 13380 100.000000 1 7245 1 chr2B.!!$F1 7244
1 TraesCS2B01G324500 chr2B 464020320 464025990 5670 False 4089.000000 6986 91.653500 883 6372 2 chr2B.!!$F3 5489
2 TraesCS2B01G324500 chr2B 463765712 463771781 6069 False 1846.900000 3507 89.703750 884 6852 4 chr2B.!!$F2 5968
3 TraesCS2B01G324500 chr2A 529791497 529797155 5658 False 2787.333333 7323 92.300667 861 6372 3 chr2A.!!$F3 5511
4 TraesCS2B01G324500 chr2A 529691199 529700283 9084 False 2504.250000 7238 91.256750 714 7245 4 chr2A.!!$F2 6531
5 TraesCS2B01G324500 chr2A 528905302 528911254 5952 False 1851.000000 3181 88.404750 884 6784 4 chr2A.!!$F1 5900
6 TraesCS2B01G324500 chr2D 392051610 392057165 5555 False 2808.000000 7012 93.726667 714 6393 3 chr2D.!!$F3 5679
7 TraesCS2B01G324500 chr2D 391849912 391855383 5471 False 2255.000000 3192 87.811667 884 6297 3 chr2D.!!$F1 5413
8 TraesCS2B01G324500 chr5B 490541394 490542103 709 True 1112.000000 1112 94.930000 1 710 1 chr5B.!!$R1 709
9 TraesCS2B01G324500 chr5B 644505417 644506126 709 True 1096.000000 1096 94.507000 1 710 1 chr5B.!!$R2 709
10 TraesCS2B01G324500 chr6B 11731693 11732402 709 True 1107.000000 1107 94.789000 1 710 1 chr6B.!!$R1 709
11 TraesCS2B01G324500 chr3B 582413453 582414162 709 True 1107.000000 1107 94.789000 1 710 1 chr3B.!!$R2 709
12 TraesCS2B01G324500 chr3B 449311844 449312553 709 True 1090.000000 1090 94.366000 1 710 1 chr3B.!!$R1 709
13 TraesCS2B01G324500 chr1B 119485795 119486504 709 True 1107.000000 1107 94.789000 1 710 1 chr1B.!!$R1 709
14 TraesCS2B01G324500 chr1B 306976735 306977444 709 False 1107.000000 1107 94.789000 1 710 1 chr1B.!!$F1 709
15 TraesCS2B01G324500 chr7B 703144741 703145450 709 True 1096.000000 1096 94.507000 1 710 1 chr7B.!!$R1 709
16 TraesCS2B01G324500 chr4B 627250956 627251665 709 True 1090.000000 1090 94.366000 1 710 1 chr4B.!!$R1 709

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
711 712 0.035820 TACAACCCACGCTCCATTCC 60.036 55.0 0.00 0.0 0.00 3.01 F
2699 3291 0.177604 AAGAGGAAGGCTCATGCTCG 59.822 55.0 2.57 0.0 39.89 5.03 F
3554 4154 0.250467 TGTCAGGGAGTTTGAGCTGC 60.250 55.0 0.00 0.0 0.00 5.25 F
4891 5547 0.874390 GTTCAGCTGATGCAACCGAA 59.126 50.0 19.04 0.0 42.74 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 3296 0.588252 GCCGCTCGTTGAATATGCAT 59.412 50.000 3.79 3.79 0.00 3.96 R
4093 4693 1.001048 GTGCTGCTTGATGCTGTTTCA 60.001 47.619 0.00 0.00 43.37 2.69 R
5253 5912 0.397941 TTCTCCCTTGCACTCAGGTG 59.602 55.000 2.31 0.00 45.53 4.00 R
6733 7454 0.513820 AAAAACCGTCGGCATACACG 59.486 50.000 12.28 0.00 35.72 4.49 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
52 53 1.459592 CGAGGCTGTCTTTGGTTAACG 59.540 52.381 0.00 0.00 0.00 3.18
64 65 1.910671 TGGTTAACGCAACTCCCCTAT 59.089 47.619 0.00 0.00 37.30 2.57
66 67 2.093341 GGTTAACGCAACTCCCCTATGA 60.093 50.000 0.00 0.00 37.30 2.15
181 182 5.980116 GCACAATACATAGAGTCTACTGTGG 59.020 44.000 19.39 13.57 34.21 4.17
188 189 3.527507 AGAGTCTACTGTGGAAGACCA 57.472 47.619 5.76 0.00 42.56 4.02
233 234 0.762418 ACATCCCGACCTTGTGTCAA 59.238 50.000 0.00 0.00 44.71 3.18
249 250 5.547465 TGTGTCAAGTTAATCGAATCCAGT 58.453 37.500 0.00 0.00 0.00 4.00
276 277 7.255242 CGGAATAAAAGATTATGCCATGACACT 60.255 37.037 0.00 0.00 44.71 3.55
279 280 9.632638 AATAAAAGATTATGCCATGACACTAGT 57.367 29.630 0.00 0.00 32.06 2.57
359 360 8.856247 CACGTGCGCAATAGTATTATTCTTATA 58.144 33.333 14.00 0.00 0.00 0.98
388 389 7.268586 AGCGAAGTTATATAAGGCTGGATATG 58.731 38.462 10.85 0.00 0.00 1.78
389 390 7.042335 GCGAAGTTATATAAGGCTGGATATGT 58.958 38.462 10.85 0.00 0.00 2.29
486 487 3.495753 GCCCAAAGCAAAAGAGATGTTTG 59.504 43.478 0.00 0.00 42.97 2.93
604 605 3.314080 GGTTTGTCAAACACCATTCTCGA 59.686 43.478 25.72 0.00 43.15 4.04
651 652 1.065854 AGAAGGGCCTCATTCTTGACG 60.066 52.381 6.46 0.00 40.63 4.35
677 678 2.450476 GTCATGAATTCCAAGGCCACT 58.550 47.619 5.01 0.00 0.00 4.00
697 698 4.215613 CACTTTGGTCTTTAGGCCTACAAC 59.784 45.833 13.46 10.70 0.00 3.32
710 711 1.369625 CTACAACCCACGCTCCATTC 58.630 55.000 0.00 0.00 0.00 2.67
711 712 0.035820 TACAACCCACGCTCCATTCC 60.036 55.000 0.00 0.00 0.00 3.01
712 713 1.303236 CAACCCACGCTCCATTCCA 60.303 57.895 0.00 0.00 0.00 3.53
743 744 2.688507 CTGTTAGGTGCGTGTCTTCAT 58.311 47.619 0.00 0.00 0.00 2.57
761 762 3.411446 TCATGTTCAGGTCAATGTCCAC 58.589 45.455 0.00 0.00 0.00 4.02
762 763 3.148412 CATGTTCAGGTCAATGTCCACA 58.852 45.455 0.00 0.00 0.00 4.17
925 935 2.949678 CGAACGTCCGATCCGCTG 60.950 66.667 0.00 0.00 0.00 5.18
1185 1255 0.314302 CGATGGAGATACCGGTGGAC 59.686 60.000 19.93 8.41 42.61 4.02
1377 1450 1.905637 TCTTTCGCTTTTCCCCTTCC 58.094 50.000 0.00 0.00 0.00 3.46
1436 1511 4.795970 ACTGTGAATTCGAAGTGTTGAC 57.204 40.909 1.32 0.00 0.00 3.18
1493 1748 1.393487 TTGTCTCGTCGGTGGTTCCA 61.393 55.000 0.00 0.00 35.57 3.53
1503 1758 2.640826 TCGGTGGTTCCAATCCTTACTT 59.359 45.455 0.00 0.00 35.57 2.24
1504 1759 3.839490 TCGGTGGTTCCAATCCTTACTTA 59.161 43.478 0.00 0.00 35.57 2.24
1505 1760 4.081309 TCGGTGGTTCCAATCCTTACTTAG 60.081 45.833 0.00 0.00 35.57 2.18
1506 1761 4.323257 CGGTGGTTCCAATCCTTACTTAGT 60.323 45.833 0.00 0.00 35.57 2.24
1507 1762 5.567430 GGTGGTTCCAATCCTTACTTAGTT 58.433 41.667 0.00 0.00 35.97 2.24
1508 1763 6.574859 CGGTGGTTCCAATCCTTACTTAGTTA 60.575 42.308 0.00 0.00 35.57 2.24
1509 1764 6.596888 GGTGGTTCCAATCCTTACTTAGTTAC 59.403 42.308 0.00 0.00 35.97 2.50
1510 1765 7.392418 GTGGTTCCAATCCTTACTTAGTTACT 58.608 38.462 0.00 0.00 0.00 2.24
1511 1766 7.333672 GTGGTTCCAATCCTTACTTAGTTACTG 59.666 40.741 0.00 0.00 0.00 2.74
1512 1767 6.822170 GGTTCCAATCCTTACTTAGTTACTGG 59.178 42.308 0.00 0.00 0.00 4.00
1513 1768 7.392418 GTTCCAATCCTTACTTAGTTACTGGT 58.608 38.462 0.00 0.00 0.00 4.00
1514 1769 6.942976 TCCAATCCTTACTTAGTTACTGGTG 58.057 40.000 0.00 0.00 0.00 4.17
1515 1770 6.727231 TCCAATCCTTACTTAGTTACTGGTGA 59.273 38.462 0.00 0.00 0.00 4.02
1687 1957 4.895297 TGAAAGAATTCCTTTGGTTGAGCT 59.105 37.500 0.65 0.00 44.63 4.09
1710 2027 6.651225 GCTGAAGTAACATTCTTTGGTAGTCT 59.349 38.462 0.00 0.00 29.45 3.24
1730 2047 3.134623 TCTTGAGCTGAAGTTGGTCTCAA 59.865 43.478 12.87 0.00 40.28 3.02
1802 2137 4.434520 GTTTTCCGGTGTTTGGATTGAAA 58.565 39.130 0.00 0.00 34.91 2.69
1810 2145 5.106442 GGTGTTTGGATTGAAACGTTTTCT 58.894 37.500 15.89 2.81 38.46 2.52
1871 2206 3.500680 TGAAAGCGTAAACAGGGACAATC 59.499 43.478 0.00 0.00 0.00 2.67
1879 2214 6.682113 GCGTAAACAGGGACAATCAGAGTATA 60.682 42.308 0.00 0.00 0.00 1.47
1881 2216 7.926555 CGTAAACAGGGACAATCAGAGTATATT 59.073 37.037 0.00 0.00 0.00 1.28
1907 2450 6.823689 ACTCCAGTAACTAATTATTGCCTGTG 59.176 38.462 0.00 0.00 28.98 3.66
1968 2519 9.734984 AATTATTGTAGGTTGTAACTGCTAAGT 57.265 29.630 0.00 0.00 38.71 2.24
1971 2522 8.773404 ATTGTAGGTTGTAACTGCTAAGTTAG 57.227 34.615 5.47 5.47 46.95 2.34
2013 2564 5.673514 TCGGTGGTAGGAAAATTATGGTAC 58.326 41.667 0.00 0.00 0.00 3.34
2042 2593 6.205658 GGTAGGATAGTTTGCTTTCATCATCC 59.794 42.308 0.00 0.00 0.00 3.51
2047 2598 4.091549 AGTTTGCTTTCATCATCCACCAT 58.908 39.130 0.00 0.00 0.00 3.55
2159 2713 5.364735 TGGTAGGGGCTATAGAAACAACTAC 59.635 44.000 3.21 8.78 0.00 2.73
2223 2803 5.975693 TTAACTCATGTTCAATTGTCCCC 57.024 39.130 5.13 0.00 37.59 4.81
2224 2804 3.814504 ACTCATGTTCAATTGTCCCCT 57.185 42.857 5.13 0.00 0.00 4.79
2508 3089 2.419574 GCAGGCAGAGGAAAACCGTATA 60.420 50.000 0.00 0.00 0.00 1.47
2694 3286 1.485895 GCTGAGAAGAGGAAGGCTCAT 59.514 52.381 0.00 0.00 36.85 2.90
2695 3287 2.742530 GCTGAGAAGAGGAAGGCTCATG 60.743 54.545 0.00 0.00 36.85 3.07
2696 3288 1.209019 TGAGAAGAGGAAGGCTCATGC 59.791 52.381 0.00 0.00 32.85 4.06
2697 3289 1.485895 GAGAAGAGGAAGGCTCATGCT 59.514 52.381 0.00 0.00 39.59 3.79
2698 3290 1.485895 AGAAGAGGAAGGCTCATGCTC 59.514 52.381 0.00 0.00 39.59 4.26
2699 3291 0.177604 AAGAGGAAGGCTCATGCTCG 59.822 55.000 2.57 0.00 39.89 5.03
2700 3292 1.227497 GAGGAAGGCTCATGCTCGG 60.227 63.158 0.00 0.00 39.59 4.63
2701 3293 2.899339 GGAAGGCTCATGCTCGGC 60.899 66.667 0.00 0.00 39.59 5.54
2702 3294 2.188994 GAAGGCTCATGCTCGGCT 59.811 61.111 0.00 0.00 39.59 5.52
2703 3295 1.886777 GAAGGCTCATGCTCGGCTC 60.887 63.158 6.14 0.00 39.59 4.70
2704 3296 2.584261 GAAGGCTCATGCTCGGCTCA 62.584 60.000 6.14 0.00 39.59 4.26
2721 3313 2.661169 GCTCATGCATATTCAACGAGCG 60.661 50.000 14.75 0.00 36.51 5.03
2997 3590 6.472887 AGAAAGCTTGCAAGGTATTACTACA 58.527 36.000 29.86 0.00 35.34 2.74
3375 3975 0.321996 AGAGACGGAAGAACAAGGGC 59.678 55.000 0.00 0.00 0.00 5.19
3554 4154 0.250467 TGTCAGGGAGTTTGAGCTGC 60.250 55.000 0.00 0.00 0.00 5.25
3670 4270 4.920640 TGCCGGTCAAAGTAAATTCAAA 57.079 36.364 1.90 0.00 0.00 2.69
3896 4496 4.058817 GGTTTCTGACGATCACAAACTCT 58.941 43.478 13.81 0.00 36.14 3.24
3993 4593 5.869344 GGTCAAAGTTCTTTGAAGCAAAAGT 59.131 36.000 23.60 0.00 41.95 2.66
4093 4693 6.174049 GCCTTCTGAGGTTAATGTTAGTTCT 58.826 40.000 0.00 0.00 45.44 3.01
4582 5236 3.373439 CAGATTTTGCAGTACTCTCTGGC 59.627 47.826 0.00 0.00 36.12 4.85
4891 5547 0.874390 GTTCAGCTGATGCAACCGAA 59.126 50.000 19.04 0.00 42.74 4.30
5209 5868 4.704833 GTGCTCCGAGCTGGCCAA 62.705 66.667 20.87 0.00 42.97 4.52
5219 5878 2.045536 CTGGCCAAGGAGCTCCAC 60.046 66.667 33.90 19.28 38.89 4.02
5253 5912 0.250467 TCAGCAGGCAGTTCAGGTTC 60.250 55.000 0.00 0.00 0.00 3.62
5426 6085 8.251750 TCAAGAAGTGATTGTAATTTCTACGG 57.748 34.615 0.00 0.00 0.00 4.02
5983 6644 1.374252 CCGTGGTACAAAGCGCTCT 60.374 57.895 12.06 0.00 44.16 4.09
6231 6935 2.194271 GGTGCAGTCGCTGTAATAGAC 58.806 52.381 8.32 0.00 39.64 2.59
6415 7135 4.298744 GCTCTTTGCTTCAGAACAAACT 57.701 40.909 6.75 0.00 38.95 2.66
6553 7274 4.274214 CACAGCAATCTCACACTTCAAAGA 59.726 41.667 0.00 0.00 0.00 2.52
6697 7418 2.338984 GGTCACCACGAAGCGAGT 59.661 61.111 0.00 0.00 0.00 4.18
6707 7428 3.562505 CACGAAGCGAGTACTTACTTGT 58.437 45.455 14.12 10.28 39.42 3.16
6733 7454 2.406452 CTTGCACCACAGGAAACGGC 62.406 60.000 0.00 0.00 0.00 5.68
6748 7469 4.807039 GGCGTGTATGCCGACGGT 62.807 66.667 16.73 0.00 46.75 4.83
6749 7470 2.812178 GCGTGTATGCCGACGGTT 60.812 61.111 16.73 6.23 36.09 4.44
6750 7471 2.385091 GCGTGTATGCCGACGGTTT 61.385 57.895 16.73 5.84 36.09 3.27
6751 7472 1.903783 GCGTGTATGCCGACGGTTTT 61.904 55.000 16.73 3.18 36.09 2.43
6752 7473 0.513820 CGTGTATGCCGACGGTTTTT 59.486 50.000 16.73 0.56 31.84 1.94
6804 7561 0.616679 TACAGCCCTCGGTAAAGCCT 60.617 55.000 0.00 0.00 34.25 4.58
6805 7562 0.616679 ACAGCCCTCGGTAAAGCCTA 60.617 55.000 0.00 0.00 34.25 3.93
6859 7633 0.601841 TTTCTCGAGCCACCGTTTCC 60.602 55.000 7.81 0.00 0.00 3.13
6889 7663 3.403057 CACTGCCGTTCGGACACG 61.403 66.667 15.69 8.72 40.02 4.49
6900 7674 1.372997 CGGACACGTGCTAGCAACT 60.373 57.895 21.29 4.01 34.81 3.16
6938 7712 4.016444 CAAACCTATGCCTCCAAGCTTTA 58.984 43.478 0.00 0.00 0.00 1.85
6944 7718 0.321298 GCCTCCAAGCTTTACCGTCA 60.321 55.000 0.00 0.00 0.00 4.35
6966 7740 0.597637 ATAGCTATGCCACGTGTCGC 60.598 55.000 15.65 12.30 0.00 5.19
6967 7741 2.622903 TAGCTATGCCACGTGTCGCC 62.623 60.000 15.65 0.33 0.00 5.54
7107 7881 3.281727 TCTGTTGGAAAAGACAGTGCT 57.718 42.857 3.73 0.00 42.90 4.40
7109 7883 3.378112 TCTGTTGGAAAAGACAGTGCTTG 59.622 43.478 3.73 0.00 42.90 4.01
7144 10479 1.510480 CTTAGGCGCTAGGCAATGGC 61.510 60.000 7.64 0.00 46.16 4.40
7177 10512 4.155826 CGCCAAAGACATAAATGGAAGTCA 59.844 41.667 0.00 0.00 34.82 3.41
7207 10558 9.699410 AATTGTCTACCCAATCAAGAAATCATA 57.301 29.630 0.00 0.00 34.01 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.303791 GGAGTTGCGTTAACCAAAGACAG 60.304 47.826 10.02 0.00 40.24 3.51
52 53 3.391296 TGGTATCTTCATAGGGGAGTTGC 59.609 47.826 0.00 0.00 0.00 4.17
64 65 7.884877 AGTGAAAATCTTCATGTGGTATCTTCA 59.115 33.333 0.00 0.00 43.39 3.02
66 67 8.641498 AAGTGAAAATCTTCATGTGGTATCTT 57.359 30.769 0.00 0.00 43.39 2.40
162 163 6.773685 GGTCTTCCACAGTAGACTCTATGTAT 59.226 42.308 0.00 0.00 39.62 2.29
181 182 6.049790 GGAACCTTACTACATCATGGTCTTC 58.950 44.000 0.00 0.00 0.00 2.87
188 189 3.704566 TCGCTGGAACCTTACTACATCAT 59.295 43.478 0.00 0.00 0.00 2.45
233 234 4.730949 TTCCGACTGGATTCGATTAACT 57.269 40.909 0.00 0.00 45.91 2.24
249 250 6.770303 TGTCATGGCATAATCTTTTATTCCGA 59.230 34.615 0.00 0.00 34.80 4.55
253 254 9.632638 ACTAGTGTCATGGCATAATCTTTTATT 57.367 29.630 1.89 0.00 0.00 1.40
276 277 0.923358 ATTTGATTGGCCCCCGACTA 59.077 50.000 0.00 0.00 0.00 2.59
279 280 1.076339 GGATTTGATTGGCCCCCGA 60.076 57.895 0.00 0.00 0.00 5.14
359 360 3.256136 AGCCTTATATAACTTCGCTCGCT 59.744 43.478 0.00 0.00 0.00 4.93
388 389 2.161211 GCAATGCCAGTCTCAGAGAAAC 59.839 50.000 0.20 0.00 0.00 2.78
389 390 2.430465 GCAATGCCAGTCTCAGAGAAA 58.570 47.619 0.20 0.00 0.00 2.52
417 418 4.911390 AGATTCGTTTCTGGGAAGACATT 58.089 39.130 0.00 0.00 0.00 2.71
464 465 3.391506 AACATCTCTTTTGCTTTGGGC 57.608 42.857 0.00 0.00 42.22 5.36
550 551 4.929146 ACAAGTATCTAGGCCAAAAGGT 57.071 40.909 5.01 0.00 0.00 3.50
651 652 2.165030 CCTTGGAATTCATGACCTGCAC 59.835 50.000 7.93 0.00 0.00 4.57
677 678 3.499021 GGGTTGTAGGCCTAAAGACCAAA 60.499 47.826 28.25 7.23 0.00 3.28
697 698 0.107017 ATCTTGGAATGGAGCGTGGG 60.107 55.000 0.00 0.00 0.00 4.61
710 711 4.739137 GCACCTAACAGCTAGAGATCTTGG 60.739 50.000 0.00 0.00 0.00 3.61
711 712 4.367450 GCACCTAACAGCTAGAGATCTTG 58.633 47.826 0.00 0.00 0.00 3.02
712 713 3.067461 CGCACCTAACAGCTAGAGATCTT 59.933 47.826 0.00 0.00 0.00 2.40
743 744 2.437651 TCTGTGGACATTGACCTGAACA 59.562 45.455 6.71 2.42 0.00 3.18
863 868 5.184287 GGGAGATTTTGGTTATTTTCACGGA 59.816 40.000 0.00 0.00 0.00 4.69
1003 1016 1.356938 GAGTTTAGTTCCTTCCGCGG 58.643 55.000 22.12 22.12 0.00 6.46
1012 1025 5.751990 TCCACTTGTTTCTCGAGTTTAGTTC 59.248 40.000 13.13 0.00 38.62 3.01
1103 1154 3.528370 CCGTCTCCCTCGCCGATT 61.528 66.667 0.00 0.00 0.00 3.34
1405 1478 1.234615 AATTCACAGTTCACGCCCCG 61.235 55.000 0.00 0.00 0.00 5.73
1436 1511 3.681897 AGTGCATAGAAAGAAAGCAGTCG 59.318 43.478 0.00 0.00 33.96 4.18
1493 1748 9.503399 CTTTTCACCAGTAACTAAGTAAGGATT 57.497 33.333 0.00 0.00 0.00 3.01
1503 1758 6.588756 CGCAACTATCTTTTCACCAGTAACTA 59.411 38.462 0.00 0.00 0.00 2.24
1504 1759 5.408604 CGCAACTATCTTTTCACCAGTAACT 59.591 40.000 0.00 0.00 0.00 2.24
1505 1760 5.178809 ACGCAACTATCTTTTCACCAGTAAC 59.821 40.000 0.00 0.00 0.00 2.50
1506 1761 5.302360 ACGCAACTATCTTTTCACCAGTAA 58.698 37.500 0.00 0.00 0.00 2.24
1507 1762 4.890088 ACGCAACTATCTTTTCACCAGTA 58.110 39.130 0.00 0.00 0.00 2.74
1508 1763 3.740115 ACGCAACTATCTTTTCACCAGT 58.260 40.909 0.00 0.00 0.00 4.00
1509 1764 3.997021 AGACGCAACTATCTTTTCACCAG 59.003 43.478 0.00 0.00 0.00 4.00
1510 1765 4.002906 AGACGCAACTATCTTTTCACCA 57.997 40.909 0.00 0.00 0.00 4.17
1511 1766 4.691216 AGAAGACGCAACTATCTTTTCACC 59.309 41.667 0.00 0.00 35.29 4.02
1512 1767 5.612865 CAGAAGACGCAACTATCTTTTCAC 58.387 41.667 0.00 0.00 35.29 3.18
1513 1768 4.152402 GCAGAAGACGCAACTATCTTTTCA 59.848 41.667 0.00 0.00 35.29 2.69
1514 1769 4.390297 AGCAGAAGACGCAACTATCTTTTC 59.610 41.667 0.00 0.00 35.29 2.29
1515 1770 4.153117 CAGCAGAAGACGCAACTATCTTTT 59.847 41.667 0.00 0.00 35.29 2.27
1622 1890 8.387354 CACAATTACTCGTATTTCACATGCTTA 58.613 33.333 0.00 0.00 0.00 3.09
1623 1891 7.119116 TCACAATTACTCGTATTTCACATGCTT 59.881 33.333 0.00 0.00 0.00 3.91
1626 1894 9.265938 CTTTCACAATTACTCGTATTTCACATG 57.734 33.333 0.00 0.00 0.00 3.21
1638 1906 3.252458 ACCCGCAACTTTCACAATTACTC 59.748 43.478 0.00 0.00 0.00 2.59
1639 1907 3.219281 ACCCGCAACTTTCACAATTACT 58.781 40.909 0.00 0.00 0.00 2.24
1687 1957 8.208224 TCAAGACTACCAAAGAATGTTACTTCA 58.792 33.333 0.00 0.00 0.00 3.02
1710 2027 3.470709 CTTGAGACCAACTTCAGCTCAA 58.529 45.455 0.00 0.00 41.67 3.02
1759 2094 4.480115 ACCCCAAACTAGAAAAGGGAAAG 58.520 43.478 16.22 4.46 42.25 2.62
1760 2095 4.546224 ACCCCAAACTAGAAAAGGGAAA 57.454 40.909 16.22 0.00 42.25 3.13
1761 2096 4.546224 AACCCCAAACTAGAAAAGGGAA 57.454 40.909 16.22 0.00 42.25 3.97
1762 2097 4.546224 AAACCCCAAACTAGAAAAGGGA 57.454 40.909 16.22 0.00 42.25 4.20
1763 2098 4.039973 GGAAAACCCCAAACTAGAAAAGGG 59.960 45.833 0.00 3.87 40.58 3.95
1802 2137 5.831525 ACCTTTTTCAATAGGGAGAAAACGT 59.168 36.000 0.00 0.00 41.77 3.99
1810 2145 8.491045 AAAATTGAGACCTTTTTCAATAGGGA 57.509 30.769 0.67 0.00 41.76 4.20
1879 2214 9.561069 CAGGCAATAATTAGTTACTGGAGTAAT 57.439 33.333 2.65 0.00 41.85 1.89
1881 2216 7.985184 CACAGGCAATAATTAGTTACTGGAGTA 59.015 37.037 14.46 0.00 0.00 2.59
1882 2217 6.823689 CACAGGCAATAATTAGTTACTGGAGT 59.176 38.462 14.46 0.00 0.00 3.85
1883 2218 7.047891 TCACAGGCAATAATTAGTTACTGGAG 58.952 38.462 14.46 8.91 0.00 3.86
1885 2220 7.624360 TTCACAGGCAATAATTAGTTACTGG 57.376 36.000 14.46 6.96 0.00 4.00
1968 2519 6.148948 CGAAACAACCTGAAATCAATGCTAA 58.851 36.000 0.00 0.00 0.00 3.09
1969 2520 5.335583 CCGAAACAACCTGAAATCAATGCTA 60.336 40.000 0.00 0.00 0.00 3.49
1971 2522 3.674753 CCGAAACAACCTGAAATCAATGC 59.325 43.478 0.00 0.00 0.00 3.56
2013 2564 6.817765 TGAAAGCAAACTATCCTACCAAAG 57.182 37.500 0.00 0.00 0.00 2.77
2047 2598 6.969993 ATGTTACTCCTAAGCAAAACCAAA 57.030 33.333 0.00 0.00 0.00 3.28
2062 2613 6.090898 CAGTACAAGTGCAAGGTATGTTACTC 59.909 42.308 0.00 0.00 31.21 2.59
2223 2803 4.437239 ACCAATCGTAGAATTGCTGAGAG 58.563 43.478 0.00 0.00 43.58 3.20
2224 2804 4.471904 ACCAATCGTAGAATTGCTGAGA 57.528 40.909 0.00 0.00 43.58 3.27
2333 2913 0.892358 CCTTTTCTGCTCAGCTGCCA 60.892 55.000 9.47 7.78 0.00 4.92
2481 3062 2.748058 TTTCCTCTGCCTGCCGAACC 62.748 60.000 0.00 0.00 0.00 3.62
2551 3132 3.292460 CGAGGGACCTCTCTGTTCTATT 58.708 50.000 15.83 0.00 40.69 1.73
2694 3286 1.202675 TGAATATGCATGAGCCGAGCA 60.203 47.619 10.16 0.00 43.14 4.26
2695 3287 1.516161 TGAATATGCATGAGCCGAGC 58.484 50.000 10.16 0.00 41.13 5.03
2696 3288 2.096565 CGTTGAATATGCATGAGCCGAG 60.097 50.000 10.16 0.00 41.13 4.63
2697 3289 1.866601 CGTTGAATATGCATGAGCCGA 59.133 47.619 10.16 0.00 41.13 5.54
2698 3290 1.866601 TCGTTGAATATGCATGAGCCG 59.133 47.619 10.16 4.33 41.13 5.52
2699 3291 2.350197 GCTCGTTGAATATGCATGAGCC 60.350 50.000 20.48 8.63 39.11 4.70
2700 3292 2.661169 CGCTCGTTGAATATGCATGAGC 60.661 50.000 20.92 20.92 40.41 4.26
2701 3293 2.096565 CCGCTCGTTGAATATGCATGAG 60.097 50.000 10.16 6.52 0.00 2.90
2702 3294 1.866601 CCGCTCGTTGAATATGCATGA 59.133 47.619 10.16 0.00 0.00 3.07
2703 3295 1.661178 GCCGCTCGTTGAATATGCATG 60.661 52.381 10.16 0.00 0.00 4.06
2704 3296 0.588252 GCCGCTCGTTGAATATGCAT 59.412 50.000 3.79 3.79 0.00 3.96
2721 3313 2.101700 GCTGCTTACAGTCATGGCC 58.898 57.895 0.00 0.00 46.30 5.36
3375 3975 1.666872 GCTGGCCTTTTTGCTGCAG 60.667 57.895 10.11 10.11 33.37 4.41
3554 4154 4.401519 TCCCTCGAGTATTGTCTTAACCAG 59.598 45.833 12.31 0.00 0.00 4.00
3670 4270 3.886505 TGTCAAAATTAACCAGCCGAGTT 59.113 39.130 0.00 0.00 0.00 3.01
3896 4496 3.846588 AGATGCTGAACCTTCTCCCTTAA 59.153 43.478 0.00 0.00 0.00 1.85
4093 4693 1.001048 GTGCTGCTTGATGCTGTTTCA 60.001 47.619 0.00 0.00 43.37 2.69
4582 5236 2.935201 GCAGACAGCTTTCTGACCATAG 59.065 50.000 29.64 5.52 45.19 2.23
4891 5547 1.139853 CTCCAGCCGAGCCTTTTATCT 59.860 52.381 0.00 0.00 0.00 1.98
5079 5735 5.449107 AAGACTCTGCGTAGTTAGAAACA 57.551 39.130 0.00 0.00 0.00 2.83
5219 5878 1.002430 TGCTGAAGGTACAGAAGCTGG 59.998 52.381 0.00 0.00 39.94 4.85
5253 5912 0.397941 TTCTCCCTTGCACTCAGGTG 59.602 55.000 2.31 0.00 45.53 4.00
5467 6128 4.638421 ACACAATGAAACTTTTCGTCCTGA 59.362 37.500 0.00 0.00 40.01 3.86
5983 6644 9.905713 AAAGTAAAGCTATATTCACATTCAGGA 57.094 29.630 0.00 0.00 0.00 3.86
6553 7274 1.414181 CCTGCCATCGTTATCCACTCT 59.586 52.381 0.00 0.00 0.00 3.24
6697 7418 4.748102 GTGCAAGCACACTACAAGTAAGTA 59.252 41.667 19.47 0.00 45.53 2.24
6733 7454 0.513820 AAAAACCGTCGGCATACACG 59.486 50.000 12.28 0.00 35.72 4.49
6804 7561 1.995376 TCTATGCCGACAGCCATCTA 58.005 50.000 0.00 0.00 42.71 1.98
6805 7562 1.123077 TTCTATGCCGACAGCCATCT 58.877 50.000 0.00 0.00 42.71 2.90
6882 7656 1.372997 AGTTGCTAGCACGTGTCCG 60.373 57.895 19.17 6.58 40.83 4.79
6889 7663 2.174349 GCACGCAGTTGCTAGCAC 59.826 61.111 19.17 12.82 41.61 4.40
6938 7712 1.970640 TGGCATAGCTATGATGACGGT 59.029 47.619 33.10 0.00 34.82 4.83
6944 7718 2.608016 CGACACGTGGCATAGCTATGAT 60.608 50.000 33.10 12.25 35.75 2.45
6973 7747 1.841302 GATGACCACCAGGAGCACCA 61.841 60.000 2.07 0.00 38.69 4.17
7100 7874 0.403271 AAGCATCTCCCAAGCACTGT 59.597 50.000 0.00 0.00 0.00 3.55
7107 7881 1.289160 AGTGGCTAAGCATCTCCCAA 58.711 50.000 0.00 0.00 0.00 4.12
7109 7883 2.224402 CCTAAGTGGCTAAGCATCTCCC 60.224 54.545 0.00 0.00 0.00 4.30
7144 10479 0.729140 GTCTTTGGCGATGCGTTTGG 60.729 55.000 0.00 0.00 0.00 3.28
7149 10484 2.823196 TTTATGTCTTTGGCGATGCG 57.177 45.000 0.00 0.00 0.00 4.73
7177 10512 8.477419 TTTCTTGATTGGGTAGACAATTTCTT 57.523 30.769 0.00 0.00 40.92 2.52
7207 10558 9.230122 TCGTTTGGTATATCAATGCAATATGAT 57.770 29.630 14.83 14.83 39.50 2.45
7215 10566 3.563808 TGGCTCGTTTGGTATATCAATGC 59.436 43.478 0.00 2.71 0.00 3.56
7220 10571 6.170506 TGGAATATGGCTCGTTTGGTATATC 58.829 40.000 0.00 0.00 0.00 1.63
7225 10576 2.799126 TGGAATATGGCTCGTTTGGT 57.201 45.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.