Multiple sequence alignment - TraesCS3D01G172600

Loading Multiple Alignment...

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 TraesCS3D01G172600 chr3D 100.000 6603 0 0 1 6603 153085136 153078534 0.000000e+00 12194
1 TraesCS3D01G172600 chr3D 91.238 2705 150 22 2018 4688 152849868 152847217 0.000000e+00 3602
2 TraesCS3D01G172600 chr3D 93.133 932 51 9 1093 2022 152850828 152849908 0.000000e+00 1354
3 TraesCS3D01G172600 chr3D 89.243 1004 56 17 4785 5752 152847161 152846174 0.000000e+00 1208
4 TraesCS3D01G172600 chr3D 86.942 605 47 14 5749 6349 152846072 152845496 0.000000e+00 651
5 TraesCS3D01G172600 chr3D 89.349 169 18 0 6435 6603 152825217 152825049 5.190000e-51 213
6 TraesCS3D01G172600 chr3D 87.023 131 15 2 4679 4809 559844827 559844955 5.340000e-31 147
7 TraesCS3D01G172600 chr3D 86.260 131 16 2 4679 4809 33460418 33460546 2.480000e-29 141
8 TraesCS3D01G172600 chr3B 94.109 2699 100 12 2018 4697 224318496 224315838 0.000000e+00 4048
9 TraesCS3D01G172600 chr3B 90.446 2062 131 34 1093 3126 224285677 224283654 0.000000e+00 2656
10 TraesCS3D01G172600 chr3B 89.660 2118 141 36 1093 3172 223676716 223674639 0.000000e+00 2627
11 TraesCS3D01G172600 chr3B 91.424 1749 95 15 1093 2831 224163217 224161514 0.000000e+00 2348
12 TraesCS3D01G172600 chr3B 93.224 1579 85 9 3124 4688 224281751 224280181 0.000000e+00 2303
13 TraesCS3D01G172600 chr3B 91.175 1575 75 24 4785 6324 224280155 224278610 0.000000e+00 2080
14 TraesCS3D01G172600 chr3B 90.863 1576 80 26 4785 6325 223661924 223660378 0.000000e+00 2054
15 TraesCS3D01G172600 chr3B 91.679 1382 81 11 3322 4688 223663312 223661950 0.000000e+00 1884
16 TraesCS3D01G172600 chr3B 94.709 1115 30 13 4777 5872 224315843 224314739 0.000000e+00 1705
17 TraesCS3D01G172600 chr3B 93.810 517 31 1 1506 2022 224319051 224318536 0.000000e+00 776
18 TraesCS3D01G172600 chr3B 93.058 533 27 5 2826 3357 224156273 224155750 0.000000e+00 771
19 TraesCS3D01G172600 chr3B 87.048 664 55 11 822 1468 224319699 224319050 0.000000e+00 721
20 TraesCS3D01G172600 chr3B 90.847 295 17 3 6314 6603 224277242 224276953 2.890000e-103 387
21 TraesCS3D01G172600 chr3B 89.761 293 17 5 6316 6603 223659025 223658741 4.870000e-96 363
22 TraesCS3D01G172600 chr3B 89.062 256 20 4 1 252 224321616 224321365 1.790000e-80 311
23 TraesCS3D01G172600 chr3B 92.821 195 13 1 629 822 224319939 224319745 1.400000e-71 281
24 TraesCS3D01G172600 chr3B 95.833 168 7 0 3159 3326 223669341 223669174 8.440000e-69 272
25 TraesCS3D01G172600 chr3B 89.706 204 15 4 5932 6130 224314199 224313997 8.500000e-64 255
26 TraesCS3D01G172600 chr3B 89.941 169 17 0 6435 6603 223964908 223964740 1.110000e-52 219
27 TraesCS3D01G172600 chr3A 93.361 2696 110 18 2015 4688 177106019 177108667 0.000000e+00 3923
28 TraesCS3D01G172600 chr3A 90.852 2711 154 23 2015 4688 177672891 177675544 0.000000e+00 3546
29 TraesCS3D01G172600 chr3A 93.438 1280 33 8 4674 5932 177108954 177110203 0.000000e+00 1851
30 TraesCS3D01G172600 chr3A 92.333 1200 61 9 822 2019 177104809 177105979 0.000000e+00 1677
31 TraesCS3D01G172600 chr3A 84.427 899 73 33 5550 6405 177676286 177677160 0.000000e+00 822
32 TraesCS3D01G172600 chr3A 86.471 717 53 17 4813 5486 177675569 177676284 0.000000e+00 747
33 TraesCS3D01G172600 chr3A 82.429 848 91 23 1 822 177103948 177104763 0.000000e+00 688
34 TraesCS3D01G172600 chr3A 92.723 481 24 3 6129 6603 177110620 177111095 0.000000e+00 684
35 TraesCS3D01G172600 chr3A 92.166 217 15 2 5915 6130 177110244 177110459 8.320000e-79 305
36 TraesCS3D01G172600 chr3A 89.349 169 18 0 6435 6603 177685666 177685834 5.190000e-51 213
37 TraesCS3D01G172600 chr3A 93.651 126 6 2 1093 1218 177672746 177672869 3.140000e-43 187
38 TraesCS3D01G172600 chr1B 91.736 242 19 1 2967 3208 345497032 345497272 1.060000e-87 335
39 TraesCS3D01G172600 chr1B 86.260 131 16 2 4679 4809 535290034 535290162 2.480000e-29 141
40 TraesCS3D01G172600 chr7B 86.822 129 17 0 4672 4800 452219544 452219672 1.920000e-30 145
41 TraesCS3D01G172600 chr7A 86.260 131 16 2 4679 4809 422260535 422260663 2.480000e-29 141
42 TraesCS3D01G172600 chr7A 86.260 131 16 2 4679 4809 561275368 561275496 2.480000e-29 141
43 TraesCS3D01G172600 chr5D 86.260 131 16 2 4679 4809 107909255 107909127 2.480000e-29 141
44 TraesCS3D01G172600 chr4B 86.260 131 16 2 4679 4809 624687076 624686948 2.480000e-29 141


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 TraesCS3D01G172600 chr3D 153078534 153085136 6602 True 12194.000000 12194 100.000000 1 6603 1 chr3D.!!$R2 6602
1 TraesCS3D01G172600 chr3D 152845496 152850828 5332 True 1703.750000 3602 90.139000 1093 6349 4 chr3D.!!$R3 5256
2 TraesCS3D01G172600 chr3B 223674639 223676716 2077 True 2627.000000 2627 89.660000 1093 3172 1 chr3B.!!$R2 2079
3 TraesCS3D01G172600 chr3B 224161514 224163217 1703 True 2348.000000 2348 91.424000 1093 2831 1 chr3B.!!$R5 1738
4 TraesCS3D01G172600 chr3B 224276953 224285677 8724 True 1856.500000 2656 91.423000 1093 6603 4 chr3B.!!$R7 5510
5 TraesCS3D01G172600 chr3B 223658741 223663312 4571 True 1433.666667 2054 90.767667 3322 6603 3 chr3B.!!$R6 3281
6 TraesCS3D01G172600 chr3B 224313997 224321616 7619 True 1156.714286 4048 91.609286 1 6130 7 chr3B.!!$R8 6129
7 TraesCS3D01G172600 chr3B 224155750 224156273 523 True 771.000000 771 93.058000 2826 3357 1 chr3B.!!$R4 531
8 TraesCS3D01G172600 chr3A 177103948 177111095 7147 False 1521.333333 3923 91.075000 1 6603 6 chr3A.!!$F2 6602
9 TraesCS3D01G172600 chr3A 177672746 177677160 4414 False 1325.500000 3546 88.850250 1093 6405 4 chr3A.!!$F3 5312

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
439 444 0.407139 AAGTTTGAGCATGGCCTCCT 59.593 50.0 3.32 0.00 0.00 3.69 F
1268 2724 0.327867 TGAAGGATGCCTGGATCCCT 60.328 55.0 9.90 1.23 42.81 4.20 F
2500 4076 0.108585 TTCCTGTCCACAGAGTTGCC 59.891 55.0 8.36 0.00 46.59 4.52 F
2681 4257 0.178900 AGGAAACGGGAGGAAGGAGT 60.179 55.0 0.00 0.00 0.00 3.85 F
2682 4258 0.249676 GGAAACGGGAGGAAGGAGTC 59.750 60.0 0.00 0.00 0.00 3.36 F
4696 8521 0.698818 ACCTCCATCCCGAAAAGCTT 59.301 50.0 0.00 0.00 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 3037 1.495878 GATGCTCACTATCCTGTGCG 58.504 55.000 0.00 0.00 37.81 5.34 R
2607 4183 2.497675 TCTTCTGCTACAGGCCTACAAG 59.502 50.000 3.98 4.13 40.92 3.16 R
4390 7901 2.031870 GCCAATTACCCCCATCAGTTC 58.968 52.381 0.00 0.00 0.00 3.01 R
4696 8521 9.952188 CATTCGTATCTAGACAAATCTAAGACA 57.048 33.333 0.00 0.00 36.98 3.41 R
4739 8564 8.355169 TGTCTAAATACGGATGTATCTAACACC 58.645 37.037 0.00 0.00 42.09 4.16 R
6519 12674 0.176680 CTCATCACCTCCACTTCCCG 59.823 60.000 0.00 0.00 0.00 5.14 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 0.901580 CATGGCTTGCCAAGGAGGTT 60.902 55.000 18.76 0.00 40.61 3.50
31 32 0.478072 AAGGAGGTTGGCATCACACA 59.522 50.000 0.00 0.00 0.00 3.72
35 36 2.255252 GTTGGCATCACACACCGC 59.745 61.111 0.00 0.00 0.00 5.68
62 63 2.737252 CGCTGTTAACAACTCCTTCTCC 59.263 50.000 10.03 0.00 0.00 3.71
82 83 0.669077 CGCGTAGTCTAGCTTCCCAT 59.331 55.000 0.00 0.00 0.00 4.00
93 94 1.875963 CTTCCCATTCGTGCCACAC 59.124 57.895 0.00 0.00 0.00 3.82
182 183 5.068198 ACATTTGTTCATGCTCACTTGTCTT 59.932 36.000 0.00 0.00 0.00 3.01
215 219 8.350722 TCGTAGATTCATGTAGGTGAATTACTC 58.649 37.037 3.90 0.00 46.02 2.59
252 256 9.754382 GCATCCAGATTATTTGTTCATTTGTAT 57.246 29.630 0.00 0.00 0.00 2.29
279 283 9.796120 TTAATAATTTGGACTTGCGGATTAAAG 57.204 29.630 0.00 0.00 0.00 1.85
291 295 4.096532 TGCGGATTAAAGTGTTGTTGAACA 59.903 37.500 0.00 0.00 39.88 3.18
352 357 5.037383 TGGAACATGGCCGTACAATATAA 57.963 39.130 0.00 0.00 0.00 0.98
439 444 0.407139 AAGTTTGAGCATGGCCTCCT 59.593 50.000 3.32 0.00 0.00 3.69
476 482 7.921786 AATTACGAAGGACATTCTGAAATGA 57.078 32.000 5.22 0.00 44.25 2.57
492 498 8.195617 TCTGAAATGATTTTGAAAACCACAAC 57.804 30.769 0.00 0.00 0.00 3.32
510 516 7.665254 CCACAACATGGCGACTCTACTAGAG 62.665 52.000 11.06 11.06 44.34 2.43
511 517 3.562343 ACATGGCGACTCTACTAGAGA 57.438 47.619 18.41 0.00 45.07 3.10
512 518 3.207778 ACATGGCGACTCTACTAGAGAC 58.792 50.000 18.41 11.80 45.07 3.36
520 526 5.707411 GACTCTACTAGAGACGTGAAGAC 57.293 47.826 18.41 0.00 45.07 3.01
521 527 5.410355 ACTCTACTAGAGACGTGAAGACT 57.590 43.478 18.41 0.00 45.07 3.24
523 529 4.505808 TCTACTAGAGACGTGAAGACTGG 58.494 47.826 0.00 0.00 0.00 4.00
524 530 3.420300 ACTAGAGACGTGAAGACTGGA 57.580 47.619 0.00 0.00 0.00 3.86
525 531 3.340034 ACTAGAGACGTGAAGACTGGAG 58.660 50.000 0.00 0.00 0.00 3.86
527 533 2.432444 AGAGACGTGAAGACTGGAGAG 58.568 52.381 0.00 0.00 0.00 3.20
528 534 2.156098 GAGACGTGAAGACTGGAGAGT 58.844 52.381 0.00 0.00 33.98 3.24
529 535 1.883275 AGACGTGAAGACTGGAGAGTG 59.117 52.381 0.00 0.00 30.16 3.51
530 536 1.609555 GACGTGAAGACTGGAGAGTGT 59.390 52.381 0.00 0.00 30.16 3.55
549 574 6.958192 AGAGTGTTCTAGTAACATTCCCCTTA 59.042 38.462 18.21 0.00 37.53 2.69
552 577 7.016858 AGTGTTCTAGTAACATTCCCCTTACAA 59.983 37.037 9.85 0.00 32.23 2.41
556 581 7.191210 TCTAGTAACATTCCCCTTACAAGGTA 58.809 38.462 7.23 0.00 44.98 3.08
589 614 1.376037 GCTCAAGTGACCGGGGAAG 60.376 63.158 6.32 0.00 0.00 3.46
591 616 2.359975 CAAGTGACCGGGGAAGGC 60.360 66.667 6.32 0.00 33.69 4.35
592 617 2.852075 AAGTGACCGGGGAAGGCA 60.852 61.111 6.32 0.00 33.69 4.75
593 618 2.231380 AAGTGACCGGGGAAGGCAT 61.231 57.895 6.32 0.00 33.69 4.40
619 670 8.770438 TTTTAAAAGTCACAAGCAAGAATGTT 57.230 26.923 0.00 0.00 0.00 2.71
652 2023 6.054860 AGAAAATCGATGGAGGAAAAGAGA 57.945 37.500 0.00 0.00 0.00 3.10
654 2025 6.597280 AGAAAATCGATGGAGGAAAAGAGAAG 59.403 38.462 0.00 0.00 0.00 2.85
665 2037 7.611855 TGGAGGAAAAGAGAAGACATTTTATCC 59.388 37.037 0.00 0.00 34.99 2.59
667 2039 8.572855 AGGAAAAGAGAAGACATTTTATCCTG 57.427 34.615 0.00 0.00 0.00 3.86
699 2071 1.618861 CGTCCTAGTCAACGAAGCTG 58.381 55.000 4.12 0.00 41.29 4.24
701 2073 1.272769 GTCCTAGTCAACGAAGCTGGT 59.727 52.381 0.00 0.00 0.00 4.00
797 2169 2.975732 ATGTCGATGAGCTGTGACAT 57.024 45.000 11.76 11.76 44.40 3.06
850 2269 1.471851 CGTGCATGTGTAATACGGGGA 60.472 52.381 0.00 0.00 0.00 4.81
851 2270 1.937899 GTGCATGTGTAATACGGGGAC 59.062 52.381 0.00 0.00 0.00 4.46
913 2332 1.755008 CCGTCTCTCTCCCCCACTC 60.755 68.421 0.00 0.00 0.00 3.51
958 2379 2.391389 GCGGAGGTTTCTCTTGCCG 61.391 63.158 0.00 0.00 39.86 5.69
971 2392 2.037620 CTTGCCGGATCAGGAGGAGG 62.038 65.000 16.86 0.00 0.00 4.30
1115 2536 2.038659 CATCCAGGTCTCTTCCTCTCC 58.961 57.143 0.00 0.00 35.37 3.71
1257 2713 5.646793 AGAACACACAAGATGATGAAGGATG 59.353 40.000 0.00 0.00 0.00 3.51
1258 2714 3.693085 ACACACAAGATGATGAAGGATGC 59.307 43.478 0.00 0.00 0.00 3.91
1259 2715 3.066342 CACACAAGATGATGAAGGATGCC 59.934 47.826 0.00 0.00 0.00 4.40
1260 2716 3.053842 ACACAAGATGATGAAGGATGCCT 60.054 43.478 0.00 0.00 33.87 4.75
1261 2717 3.315470 CACAAGATGATGAAGGATGCCTG 59.685 47.826 0.00 0.00 32.13 4.85
1262 2718 2.885266 CAAGATGATGAAGGATGCCTGG 59.115 50.000 0.00 0.00 32.13 4.45
1263 2719 2.415624 AGATGATGAAGGATGCCTGGA 58.584 47.619 0.00 0.00 32.13 3.86
1264 2720 2.987437 AGATGATGAAGGATGCCTGGAT 59.013 45.455 0.00 0.00 32.13 3.41
1265 2721 2.945080 TGATGAAGGATGCCTGGATC 57.055 50.000 0.00 0.00 32.13 3.36
1266 2722 1.422781 TGATGAAGGATGCCTGGATCC 59.577 52.381 4.20 4.20 42.21 3.36
1267 2723 0.776176 ATGAAGGATGCCTGGATCCC 59.224 55.000 9.90 1.22 42.81 3.85
1268 2724 0.327867 TGAAGGATGCCTGGATCCCT 60.328 55.000 9.90 1.23 42.81 4.20
1269 2725 1.061424 TGAAGGATGCCTGGATCCCTA 60.061 52.381 9.90 0.00 42.81 3.53
1270 2726 2.273619 GAAGGATGCCTGGATCCCTAT 58.726 52.381 9.90 1.62 42.81 2.57
1271 2727 2.447582 AGGATGCCTGGATCCCTATT 57.552 50.000 9.90 0.00 42.81 1.73
1272 2728 2.723342 AGGATGCCTGGATCCCTATTT 58.277 47.619 9.90 0.00 42.81 1.40
1273 2729 2.377869 AGGATGCCTGGATCCCTATTTG 59.622 50.000 9.90 0.00 42.81 2.32
1274 2730 2.376518 GGATGCCTGGATCCCTATTTGA 59.623 50.000 9.90 0.00 36.61 2.69
1275 2731 3.181429 GGATGCCTGGATCCCTATTTGAA 60.181 47.826 9.90 0.00 36.61 2.69
1276 2732 4.509843 GGATGCCTGGATCCCTATTTGAAT 60.510 45.833 9.90 0.00 36.61 2.57
1277 2733 5.281193 GGATGCCTGGATCCCTATTTGAATA 60.281 44.000 9.90 0.00 36.61 1.75
1278 2734 5.865977 TGCCTGGATCCCTATTTGAATAT 57.134 39.130 9.90 0.00 0.00 1.28
1283 2739 7.094032 GCCTGGATCCCTATTTGAATATTCTTG 60.094 40.741 16.24 0.00 0.00 3.02
1504 3006 0.449388 CGAGTCTTGCCTTGGATTGC 59.551 55.000 0.00 0.00 0.00 3.56
1511 3013 2.123428 GCCTTGGATTGCGATGCCT 61.123 57.895 2.59 0.00 0.00 4.75
1554 3056 1.067669 TCGCACAGGATAGTGAGCATC 59.932 52.381 0.00 0.00 42.05 3.91
1661 3164 1.831106 TGGTGATATGTCTCGGTTGCT 59.169 47.619 0.00 0.00 0.00 3.91
1675 3178 2.355756 CGGTTGCTAATTCCATGTCTGG 59.644 50.000 0.00 0.00 44.64 3.86
1695 3198 7.093333 TGTCTGGATTCAGCATAACTAAAGAGA 60.093 37.037 0.00 0.00 40.69 3.10
1726 3229 9.101655 CCTTCAAATCTGTTTGTTTTTCTTGAT 57.898 29.630 1.38 0.00 44.03 2.57
1747 3250 7.800155 TGATTACTTCACAAATCAGAACACA 57.200 32.000 0.00 0.00 37.23 3.72
1991 3500 6.259829 ACAATTTAACCTTGGTTGATGCAAAC 59.740 34.615 14.67 0.00 0.00 2.93
1995 3504 4.584327 ACCTTGGTTGATGCAAACTAAC 57.416 40.909 0.00 0.00 31.53 2.34
2414 3990 7.683222 GCATTCAGCTGTTCTAGTACATAGACT 60.683 40.741 14.67 0.00 39.20 3.24
2415 3991 7.704578 TTCAGCTGTTCTAGTACATAGACTT 57.295 36.000 14.67 0.00 40.33 3.01
2461 4037 5.563085 CGGTATTCTAGCTAGTGTCCATGAC 60.563 48.000 20.10 8.23 0.00 3.06
2500 4076 0.108585 TTCCTGTCCACAGAGTTGCC 59.891 55.000 8.36 0.00 46.59 4.52
2520 4096 1.821936 TGCTTTTTGGCAGTGGTGG 59.178 52.632 0.00 0.00 37.29 4.61
2607 4183 0.912486 AGACCAAGGACATAGGTGCC 59.088 55.000 0.00 0.00 35.71 5.01
2630 4206 1.825474 GTAGGCCTGTAGCAGAAGACA 59.175 52.381 17.99 0.00 46.50 3.41
2681 4257 0.178900 AGGAAACGGGAGGAAGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
2682 4258 0.249676 GGAAACGGGAGGAAGGAGTC 59.750 60.000 0.00 0.00 0.00 3.36
2684 4260 1.624312 GAAACGGGAGGAAGGAGTCTT 59.376 52.381 0.00 0.00 35.62 3.01
2687 4263 2.898662 ACGGGAGGAAGGAGTCTTTTA 58.101 47.619 0.00 0.00 32.52 1.52
2688 4264 2.832733 ACGGGAGGAAGGAGTCTTTTAG 59.167 50.000 0.00 0.00 32.52 1.85
2689 4265 2.168728 CGGGAGGAAGGAGTCTTTTAGG 59.831 54.545 0.00 0.00 32.52 2.69
2690 4266 3.451890 GGGAGGAAGGAGTCTTTTAGGA 58.548 50.000 0.00 0.00 32.52 2.94
2770 4348 7.224297 TGTATCTTGCTAGGAAAAGTCAAAGT 58.776 34.615 0.00 0.00 0.00 2.66
2771 4349 7.719633 TGTATCTTGCTAGGAAAAGTCAAAGTT 59.280 33.333 0.00 0.00 0.00 2.66
2772 4350 7.588497 ATCTTGCTAGGAAAAGTCAAAGTTT 57.412 32.000 0.00 0.00 0.00 2.66
2773 4351 7.027778 TCTTGCTAGGAAAAGTCAAAGTTTC 57.972 36.000 0.00 0.00 33.78 2.78
2774 4352 6.601613 TCTTGCTAGGAAAAGTCAAAGTTTCA 59.398 34.615 0.00 0.00 35.80 2.69
2775 4353 6.767524 TGCTAGGAAAAGTCAAAGTTTCAA 57.232 33.333 0.00 0.00 35.80 2.69
2776 4354 7.164230 TGCTAGGAAAAGTCAAAGTTTCAAA 57.836 32.000 0.00 0.00 35.80 2.69
2777 4355 7.781056 TGCTAGGAAAAGTCAAAGTTTCAAAT 58.219 30.769 0.00 0.00 35.80 2.32
2805 4387 6.378661 AAGCACCCATTATATAGAGATGCA 57.621 37.500 0.00 0.00 32.99 3.96
2920 4514 3.293311 TCAGTACGTTAGTTGTCCTGC 57.707 47.619 0.00 0.00 0.00 4.85
2938 4532 3.560025 CCTGCTGTGGATAAAGGTTCACT 60.560 47.826 0.00 0.00 0.00 3.41
3013 4607 2.128035 GGACATATTCCTGAACGCTCG 58.872 52.381 0.00 0.00 41.95 5.03
3073 4668 3.825585 TCAATTGTGCTTGCAGGATTGTA 59.174 39.130 20.32 11.23 0.00 2.41
3407 6907 5.541953 CTGGTGATCTCCAGTCATTATCA 57.458 43.478 28.32 0.27 46.92 2.15
3554 7055 7.647715 ACATGTGTTTTTGTTAAGGAATCTTCG 59.352 33.333 0.00 0.00 34.59 3.79
3566 7067 8.678199 GTTAAGGAATCTTCGAAAGGATTTGAT 58.322 33.333 12.36 1.86 34.63 2.57
3786 7287 4.224594 ACTCATCTCTGAAATCAGCCTTCA 59.775 41.667 5.53 0.00 43.46 3.02
3941 7444 6.956202 TGGCATGGTTTTTCATTTCAAATT 57.044 29.167 0.00 0.00 0.00 1.82
4135 7643 7.771183 TGTAAGTCATTTTCTCAAGCTGTTTT 58.229 30.769 0.00 0.00 0.00 2.43
4153 7661 7.064966 AGCTGTTTTTCTTTTCCAAATGTCAAG 59.935 33.333 0.00 0.00 0.00 3.02
4206 7716 9.255304 TGTTTAAAGGAAGTTGAAATGTTATGC 57.745 29.630 0.00 0.00 0.00 3.14
4207 7717 9.255304 GTTTAAAGGAAGTTGAAATGTTATGCA 57.745 29.630 0.00 0.00 0.00 3.96
4284 7795 8.764365 TGGCTGTCCATAATTCGAATGAATTGT 61.764 37.037 12.25 4.24 44.43 2.71
4387 7898 8.164153 GTGCATGCTCTTTTATTAATGTTGTTG 58.836 33.333 20.33 0.00 0.00 3.33
4696 8521 0.698818 ACCTCCATCCCGAAAAGCTT 59.301 50.000 0.00 0.00 0.00 3.74
4739 8564 5.570344 ACGAATGTATCTAGACACGTCTTG 58.430 41.667 4.79 3.62 40.93 3.02
4759 8584 7.208080 GTCTTGGTGTTAGATACATCCGTATT 58.792 38.462 0.00 0.00 38.48 1.89
4867 8692 4.385358 AAACCAGTTTGAGATGCGTTTT 57.615 36.364 0.00 0.00 0.00 2.43
5107 8959 2.744202 CTCATGGTTAAGTGTGACCTGC 59.256 50.000 0.00 0.00 34.44 4.85
5629 9512 2.894126 GGGATACAGACCTGATCGTCAT 59.106 50.000 3.76 0.00 35.07 3.06
5660 9545 1.486726 CTGGTCTGGTCTGTATTCCCC 59.513 57.143 0.00 0.00 0.00 4.81
5773 9785 4.356405 TGAATGAGAGGAAGAGTGCAAA 57.644 40.909 0.00 0.00 0.00 3.68
5791 9803 6.207417 AGTGCAAATAGCTGACATTACAAAGT 59.793 34.615 0.00 0.00 45.94 2.66
6151 10918 8.970691 AATAGTATGTTGCTGAAATTGTGAAC 57.029 30.769 0.00 0.00 0.00 3.18
6265 11032 3.636300 TCCATCTTTCCAACCAAACACAG 59.364 43.478 0.00 0.00 0.00 3.66
6328 11096 2.017049 CAGATGAATGAAACCGACCCC 58.983 52.381 0.00 0.00 0.00 4.95
6359 12506 5.920193 TGAAACTCCATTCCATTCCATTC 57.080 39.130 0.00 0.00 0.00 2.67
6360 12507 4.711355 TGAAACTCCATTCCATTCCATTCC 59.289 41.667 0.00 0.00 0.00 3.01
6361 12508 4.335735 AACTCCATTCCATTCCATTCCA 57.664 40.909 0.00 0.00 0.00 3.53
6362 12509 4.547886 ACTCCATTCCATTCCATTCCAT 57.452 40.909 0.00 0.00 0.00 3.41
6363 12510 4.887367 ACTCCATTCCATTCCATTCCATT 58.113 39.130 0.00 0.00 0.00 3.16
6381 12531 3.504863 CATTTGGCTCCTCATTCAAACG 58.495 45.455 0.00 0.00 32.87 3.60
6399 12549 1.455383 CGCACCCTTTGTTGCCTCTT 61.455 55.000 0.00 0.00 0.00 2.85
6410 12560 0.040058 TTGCCTCTTCCCACATGCAT 59.960 50.000 0.00 0.00 0.00 3.96
6415 12565 2.422377 CCTCTTCCCACATGCATGATCA 60.422 50.000 32.75 10.63 0.00 2.92
6472 12627 4.689062 TCCTAGACCCTGAACTGAGAAAT 58.311 43.478 0.00 0.00 0.00 2.17
6481 12636 0.798776 AACTGAGAAATTCGGCAGCG 59.201 50.000 15.28 0.00 35.44 5.18
6501 12656 2.031245 CGCAAGTGCACCAACTATTGAA 60.031 45.455 14.63 0.00 42.21 2.69
6519 12674 1.859080 GAAATACTCATCGTCCCGTGC 59.141 52.381 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.601841 AGTTGTTAACAGCGGACGGG 60.602 55.000 15.61 0.00 32.04 5.28
47 48 0.245539 CGCGGGAGAAGGAGTTGTTA 59.754 55.000 0.00 0.00 0.00 2.41
62 63 1.359475 GGGAAGCTAGACTACGCGG 59.641 63.158 12.47 0.00 0.00 6.46
82 83 4.980805 GGCGAGGTGTGGCACGAA 62.981 66.667 13.77 0.00 34.83 3.85
93 94 3.686045 GGGATCTAGCGGGCGAGG 61.686 72.222 0.97 0.00 0.00 4.63
182 183 7.504574 TCACCTACATGAATCTACGATAAAGGA 59.495 37.037 0.00 0.00 0.00 3.36
215 219 3.880047 ATCTGGATGCAACAAATGGTG 57.120 42.857 0.00 0.00 35.41 4.17
253 257 9.796120 CTTTAATCCGCAAGTCCAAATTATTAA 57.204 29.630 0.00 0.00 0.00 1.40
254 258 8.962679 ACTTTAATCCGCAAGTCCAAATTATTA 58.037 29.630 0.00 0.00 0.00 0.98
255 259 7.759433 CACTTTAATCCGCAAGTCCAAATTATT 59.241 33.333 0.00 0.00 30.48 1.40
256 260 7.093945 ACACTTTAATCCGCAAGTCCAAATTAT 60.094 33.333 0.00 0.00 30.48 1.28
257 261 6.207810 ACACTTTAATCCGCAAGTCCAAATTA 59.792 34.615 0.00 0.00 30.48 1.40
258 262 5.010617 ACACTTTAATCCGCAAGTCCAAATT 59.989 36.000 0.00 0.00 30.48 1.82
259 263 4.522789 ACACTTTAATCCGCAAGTCCAAAT 59.477 37.500 0.00 0.00 30.48 2.32
260 264 3.886505 ACACTTTAATCCGCAAGTCCAAA 59.113 39.130 0.00 0.00 30.48 3.28
261 265 3.482436 ACACTTTAATCCGCAAGTCCAA 58.518 40.909 0.00 0.00 30.48 3.53
262 266 3.134574 ACACTTTAATCCGCAAGTCCA 57.865 42.857 0.00 0.00 30.48 4.02
263 267 3.252458 ACAACACTTTAATCCGCAAGTCC 59.748 43.478 0.00 0.00 30.48 3.85
264 268 4.483476 ACAACACTTTAATCCGCAAGTC 57.517 40.909 0.00 0.00 30.48 3.01
265 269 4.336993 TCAACAACACTTTAATCCGCAAGT 59.663 37.500 0.00 0.00 33.29 3.16
271 275 9.092876 TCAAAATGTTCAACAACACTTTAATCC 57.907 29.630 0.00 0.00 45.47 3.01
314 319 7.496591 GCCATGTTCCATCAATGTAATTCAAAT 59.503 33.333 0.00 0.00 31.22 2.32
411 416 6.608808 AGGCCATGCTCAAACTTAGATTTATT 59.391 34.615 5.01 0.00 0.00 1.40
412 417 6.131961 AGGCCATGCTCAAACTTAGATTTAT 58.868 36.000 5.01 0.00 0.00 1.40
418 423 2.019984 GGAGGCCATGCTCAAACTTAG 58.980 52.381 5.01 0.00 0.00 2.18
454 459 7.921786 AATCATTTCAGAATGTCCTTCGTAA 57.078 32.000 0.00 0.00 42.61 3.18
465 471 8.961294 TGTGGTTTTCAAAATCATTTCAGAAT 57.039 26.923 0.00 0.00 0.00 2.40
466 472 8.663911 GTTGTGGTTTTCAAAATCATTTCAGAA 58.336 29.630 0.00 0.00 0.00 3.02
492 498 2.222213 CGTCTCTAGTAGAGTCGCCATG 59.778 54.545 26.20 10.94 44.07 3.66
498 504 5.290158 CAGTCTTCACGTCTCTAGTAGAGTC 59.710 48.000 23.51 18.04 42.83 3.36
510 516 1.609555 ACACTCTCCAGTCTTCACGTC 59.390 52.381 0.00 0.00 0.00 4.34
511 517 1.693627 ACACTCTCCAGTCTTCACGT 58.306 50.000 0.00 0.00 0.00 4.49
512 518 2.294791 AGAACACTCTCCAGTCTTCACG 59.705 50.000 0.00 0.00 31.61 4.35
513 519 4.521256 ACTAGAACACTCTCCAGTCTTCAC 59.479 45.833 0.00 0.00 31.61 3.18
515 521 6.207025 TGTTACTAGAACACTCTCCAGTCTTC 59.793 42.308 0.00 0.00 32.70 2.87
516 522 6.069331 TGTTACTAGAACACTCTCCAGTCTT 58.931 40.000 0.00 0.00 32.70 3.01
518 524 5.961396 TGTTACTAGAACACTCTCCAGTC 57.039 43.478 0.00 0.00 32.70 3.51
519 525 6.071278 GGAATGTTACTAGAACACTCTCCAGT 60.071 42.308 12.77 0.00 31.86 4.00
520 526 6.334202 GGAATGTTACTAGAACACTCTCCAG 58.666 44.000 12.77 0.00 31.86 3.86
521 527 5.187186 GGGAATGTTACTAGAACACTCTCCA 59.813 44.000 19.93 0.00 32.57 3.86
523 529 5.422650 AGGGGAATGTTACTAGAACACTCTC 59.577 44.000 12.77 10.24 32.70 3.20
524 530 5.342866 AGGGGAATGTTACTAGAACACTCT 58.657 41.667 12.77 4.66 35.52 3.24
525 531 5.678955 AGGGGAATGTTACTAGAACACTC 57.321 43.478 0.00 2.57 32.37 3.51
527 533 6.704310 TGTAAGGGGAATGTTACTAGAACAC 58.296 40.000 0.00 0.00 32.37 3.32
528 534 6.938698 TGTAAGGGGAATGTTACTAGAACA 57.061 37.500 0.00 3.45 31.54 3.18
529 535 6.822170 CCTTGTAAGGGGAATGTTACTAGAAC 59.178 42.308 0.00 0.00 42.66 3.01
530 536 6.954232 CCTTGTAAGGGGAATGTTACTAGAA 58.046 40.000 0.00 0.00 42.66 2.10
549 574 8.494433 TGAGCTAAAATTATCCATCTACCTTGT 58.506 33.333 0.00 0.00 0.00 3.16
552 577 8.718656 ACTTGAGCTAAAATTATCCATCTACCT 58.281 33.333 0.00 0.00 0.00 3.08
556 581 7.500559 GGTCACTTGAGCTAAAATTATCCATCT 59.499 37.037 1.08 0.00 39.31 2.90
589 614 5.982465 TGCTTGTGACTTTTAAAAATGCC 57.018 34.783 1.66 0.00 0.00 4.40
591 616 9.640974 CATTCTTGCTTGTGACTTTTAAAAATG 57.359 29.630 1.66 0.00 0.00 2.32
592 617 9.382275 ACATTCTTGCTTGTGACTTTTAAAAAT 57.618 25.926 1.66 0.00 0.00 1.82
593 618 8.770438 ACATTCTTGCTTGTGACTTTTAAAAA 57.230 26.923 1.66 0.00 0.00 1.94
636 2007 4.193826 TGTCTTCTCTTTTCCTCCATCG 57.806 45.455 0.00 0.00 0.00 3.84
648 2019 5.707066 AGCCAGGATAAAATGTCTTCTCT 57.293 39.130 0.00 0.00 0.00 3.10
652 2023 5.354234 CGTGTAAGCCAGGATAAAATGTCTT 59.646 40.000 0.00 0.00 0.00 3.01
654 2025 4.035208 CCGTGTAAGCCAGGATAAAATGTC 59.965 45.833 0.00 0.00 0.00 3.06
665 2037 1.445582 GACGGTCCGTGTAAGCCAG 60.446 63.158 24.45 0.00 41.37 4.85
667 2039 1.315257 TAGGACGGTCCGTGTAAGCC 61.315 60.000 24.45 16.33 42.75 4.35
854 2273 4.619140 GATGCGGGAATGCGCTGC 62.619 66.667 9.73 3.63 37.81 5.25
855 2274 2.890109 GAGATGCGGGAATGCGCTG 61.890 63.158 9.73 0.00 37.81 5.18
913 2332 2.029666 GCGTCTGGATGGATCGGG 59.970 66.667 0.00 0.00 0.00 5.14
958 2379 3.044894 ACTGATTTCCTCCTCCTGATCC 58.955 50.000 0.00 0.00 0.00 3.36
971 2392 4.214437 CACTCACAAGCGAAACTGATTTC 58.786 43.478 0.00 0.00 40.83 2.17
1257 2713 6.488715 AGAATATTCAAATAGGGATCCAGGC 58.511 40.000 15.23 0.00 0.00 4.85
1258 2714 7.946776 ACAAGAATATTCAAATAGGGATCCAGG 59.053 37.037 15.23 0.00 0.00 4.45
1259 2715 8.930846 ACAAGAATATTCAAATAGGGATCCAG 57.069 34.615 15.23 0.00 0.00 3.86
1260 2716 9.135189 CAACAAGAATATTCAAATAGGGATCCA 57.865 33.333 15.23 0.00 0.00 3.41
1261 2717 9.136323 ACAACAAGAATATTCAAATAGGGATCC 57.864 33.333 17.56 1.92 0.00 3.36
1271 2727 9.500785 TGTGATGTCTACAACAAGAATATTCAA 57.499 29.630 17.56 0.00 42.37 2.69
1272 2728 8.935844 GTGTGATGTCTACAACAAGAATATTCA 58.064 33.333 17.56 0.00 42.37 2.57
1273 2729 9.155975 AGTGTGATGTCTACAACAAGAATATTC 57.844 33.333 7.41 7.41 42.37 1.75
1277 2733 9.507329 AATTAGTGTGATGTCTACAACAAGAAT 57.493 29.630 0.00 0.00 42.37 2.40
1278 2734 8.902540 AATTAGTGTGATGTCTACAACAAGAA 57.097 30.769 0.00 0.00 42.37 2.52
1437 2938 3.571401 CCATGGGGCAGAGAATGATTTAC 59.429 47.826 2.85 0.00 0.00 2.01
1504 3006 5.920273 ACATCAAGTTGTTTTAAAGGCATCG 59.080 36.000 2.11 0.00 0.00 3.84
1511 3013 9.123709 GCGATTATCACATCAAGTTGTTTTAAA 57.876 29.630 2.11 0.00 0.00 1.52
1535 3037 1.495878 GATGCTCACTATCCTGTGCG 58.504 55.000 0.00 0.00 37.81 5.34
1554 3056 1.750193 AGGTATTTGACATGCCACCG 58.250 50.000 0.00 0.00 0.00 4.94
1675 3178 6.587273 AGGGTCTCTTTAGTTATGCTGAATC 58.413 40.000 0.00 0.00 0.00 2.52
1726 3229 9.944663 GTTAATGTGTTCTGATTTGTGAAGTAA 57.055 29.630 0.00 0.00 0.00 2.24
1728 3231 7.995289 TGTTAATGTGTTCTGATTTGTGAAGT 58.005 30.769 0.00 0.00 0.00 3.01
1955 3464 6.989759 CCAAGGTTAAATTGTTGGTAAGCTTT 59.010 34.615 3.20 0.00 41.29 3.51
1991 3500 2.755103 GGCCAAGGACAAGAATGGTTAG 59.245 50.000 0.00 0.00 35.34 2.34
1995 3504 2.806945 TAGGCCAAGGACAAGAATGG 57.193 50.000 5.01 0.00 36.00 3.16
2414 3990 9.607988 ACCGATTATGAGTTTGATATTACACAA 57.392 29.630 0.00 0.00 0.00 3.33
2461 4037 5.661759 AGGAAAGTACTAGGACAACCATAGG 59.338 44.000 8.10 0.00 38.94 2.57
2520 4096 5.019498 GCAACATACTAATGCGTACAACAC 58.981 41.667 0.00 0.00 36.50 3.32
2607 4183 2.497675 TCTTCTGCTACAGGCCTACAAG 59.502 50.000 3.98 4.13 40.92 3.16
2630 4206 4.630644 AATCCTTGTCTGACACATGACT 57.369 40.909 10.56 0.00 33.90 3.41
2805 4387 8.328758 TGTTCCTTCCTGAAACATAGATACATT 58.671 33.333 0.00 0.00 0.00 2.71
2920 4514 6.231211 ACAAGTAGTGAACCTTTATCCACAG 58.769 40.000 0.00 0.00 32.35 3.66
2938 4532 6.316640 TGTTTTACAGCTGTTAGCAACAAGTA 59.683 34.615 27.06 0.00 45.56 2.24
3073 4668 5.680619 TGCTTAATTGGAATACAGTCCGAT 58.319 37.500 0.00 0.00 42.74 4.18
3375 6875 3.009363 TGGAGATCACCAGCAAATTCTGA 59.991 43.478 7.91 0.00 36.19 3.27
3407 6907 2.158564 CCCTACAGCCATTGATGACCAT 60.159 50.000 0.00 0.00 0.00 3.55
3515 7016 8.691797 ACAAAAACACATGTAACTAGTTGGAAT 58.308 29.630 18.56 6.09 0.00 3.01
3539 7040 7.663905 TCAAATCCTTTCGAAGATTCCTTAACA 59.336 33.333 11.70 0.00 35.04 2.41
3552 7053 4.118093 TCGTGCTATCAAATCCTTTCGA 57.882 40.909 0.00 0.00 0.00 3.71
3554 7055 7.897575 ATCTATCGTGCTATCAAATCCTTTC 57.102 36.000 0.00 0.00 0.00 2.62
3566 7067 4.237724 GTGCAGCATTATCTATCGTGCTA 58.762 43.478 0.00 0.00 45.42 3.49
3941 7444 5.559770 TGTTGAGATATTTGGAACTGCTGA 58.440 37.500 0.00 0.00 0.00 4.26
4123 7630 6.966435 TTTGGAAAAGAAAAACAGCTTGAG 57.034 33.333 0.00 0.00 0.00 3.02
4135 7643 6.773976 AGTGTCTTGACATTTGGAAAAGAA 57.226 33.333 6.74 0.00 0.00 2.52
4206 7716 8.882736 TCAGTCAGTACATTAAGCATAAATGTG 58.117 33.333 16.88 1.58 44.94 3.21
4207 7717 9.448438 TTCAGTCAGTACATTAAGCATAAATGT 57.552 29.630 13.58 13.58 46.49 2.71
4256 7767 6.266103 ATTCATTCGAATTATGGACAGCCAAT 59.734 34.615 8.21 0.00 42.71 3.16
4332 7843 5.242838 ACTCACAAAAACACTGACCAAAAGA 59.757 36.000 0.00 0.00 0.00 2.52
4387 7898 3.954258 CCAATTACCCCCATCAGTTCTTC 59.046 47.826 0.00 0.00 0.00 2.87
4390 7901 2.031870 GCCAATTACCCCCATCAGTTC 58.968 52.381 0.00 0.00 0.00 3.01
4696 8521 9.952188 CATTCGTATCTAGACAAATCTAAGACA 57.048 33.333 0.00 0.00 36.98 3.41
4736 8561 9.193133 CTAAATACGGATGTATCTAACACCAAG 57.807 37.037 0.00 0.00 42.09 3.61
4739 8564 8.355169 TGTCTAAATACGGATGTATCTAACACC 58.645 37.037 0.00 0.00 42.09 4.16
4759 8584 6.959639 AAAGCTTGTCTTGGATTTGTCTAA 57.040 33.333 0.00 0.00 34.67 2.10
4867 8692 5.184287 GGCAGCAACTTAGGGTTTATAACAA 59.816 40.000 0.00 0.00 35.74 2.83
4996 8821 9.469097 AAGACTATGACTGTATCTGTCTTAACT 57.531 33.333 13.30 6.11 39.22 2.24
5660 9545 9.786105 CTCTATATGCATGTATGAGTAAGACTG 57.214 37.037 10.16 0.00 0.00 3.51
5752 9764 4.356405 TTTGCACTCTTCCTCTCATTCA 57.644 40.909 0.00 0.00 0.00 2.57
5773 9785 7.390440 TGCTTAACACTTTGTAATGTCAGCTAT 59.610 33.333 0.00 0.00 36.59 2.97
5791 9803 4.118410 CACAGTTTTGCCATTGCTTAACA 58.882 39.130 8.50 0.00 38.71 2.41
6147 10914 9.549509 GTACAATCAAAACAATTATAGCGTTCA 57.450 29.630 0.00 0.00 0.00 3.18
6151 10918 9.335891 TGTTGTACAATCAAAACAATTATAGCG 57.664 29.630 12.26 0.00 35.72 4.26
6218 10985 6.829229 TGAGACAAATTTGATTCAGCTCAT 57.171 33.333 24.64 0.00 0.00 2.90
6265 11032 8.403236 AGGTATAAAATGTTATTGTTTCGCTCC 58.597 33.333 0.00 0.00 32.10 4.70
6328 11096 6.588719 TGGAATGGAGTTTCATGGTTAAAG 57.411 37.500 0.00 0.00 0.00 1.85
6359 12506 3.674138 CGTTTGAATGAGGAGCCAAATGG 60.674 47.826 0.00 0.00 33.97 3.16
6360 12507 3.504863 CGTTTGAATGAGGAGCCAAATG 58.495 45.455 0.00 0.00 32.16 2.32
6361 12508 2.094545 GCGTTTGAATGAGGAGCCAAAT 60.095 45.455 0.00 0.00 32.16 2.32
6362 12509 1.269448 GCGTTTGAATGAGGAGCCAAA 59.731 47.619 0.00 0.00 0.00 3.28
6363 12510 0.881118 GCGTTTGAATGAGGAGCCAA 59.119 50.000 0.00 0.00 0.00 4.52
6381 12531 0.315251 GAAGAGGCAACAAAGGGTGC 59.685 55.000 0.00 0.00 41.41 5.01
6399 12549 2.440253 TCATCTGATCATGCATGTGGGA 59.560 45.455 25.43 18.25 0.00 4.37
6410 12560 5.473066 TGTGTGTCTTCTTCATCTGATCA 57.527 39.130 0.00 0.00 0.00 2.92
6415 12565 7.332926 GTCAATGTATGTGTGTCTTCTTCATCT 59.667 37.037 0.00 0.00 0.00 2.90
6481 12636 3.641437 TTCAATAGTTGGTGCACTTGC 57.359 42.857 17.98 6.87 42.50 4.01
6519 12674 0.176680 CTCATCACCTCCACTTCCCG 59.823 60.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.