Multiple sequence alignment - TraesCS4B01G164100

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 TraesCS4B01G164100 chr4B 100.000 3230 0 0 1 3230 339472675 339475904 0.000000e+00 5965.0
1 TraesCS4B01G164100 chr6A 81.028 2530 438 24 724 3230 2157168 2159678 0.000000e+00 1975.0
2 TraesCS4B01G164100 chr6A 83.827 1317 195 11 750 2054 39436306 39434996 0.000000e+00 1236.0
3 TraesCS4B01G164100 chr6A 82.212 1130 189 6 2112 3230 39434986 39433858 0.000000e+00 963.0
4 TraesCS4B01G164100 chr1A 79.537 2546 455 45 725 3230 527674825 527677344 0.000000e+00 1755.0
5 TraesCS4B01G164100 chr1B 79.544 2542 444 38 724 3220 379626468 379623958 0.000000e+00 1744.0
6 TraesCS4B01G164100 chr1B 82.201 1708 273 17 1543 3230 480458962 480460658 0.000000e+00 1441.0
7 TraesCS4B01G164100 chr1B 75.000 160 29 4 2152 2301 115446188 115446030 2.690000e-06 63.9
8 TraesCS4B01G164100 chr3B 79.293 2545 453 49 725 3230 495716528 495714019 0.000000e+00 1712.0
9 TraesCS4B01G164100 chr3B 88.889 639 70 1 1 638 55705903 55706541 0.000000e+00 785.0
10 TraesCS4B01G164100 chr2D 82.818 1455 227 13 725 2161 296705783 296707232 0.000000e+00 1280.0
11 TraesCS4B01G164100 chr2D 82.738 168 29 0 1210 1377 597688765 597688932 2.010000e-32 150.0
12 TraesCS4B01G164100 chr2D 100.000 29 0 0 977 1005 102000016 102000044 2.000000e-03 54.7
13 TraesCS4B01G164100 chr4A 94.679 639 29 3 1 638 742975227 742975861 0.000000e+00 987.0
14 TraesCS4B01G164100 chr4A 75.148 1179 246 33 801 1947 478163501 478162338 7.990000e-141 510.0
15 TraesCS4B01G164100 chr1D 93.897 639 38 1 1 638 420101548 420102186 0.000000e+00 963.0
16 TraesCS4B01G164100 chr5B 80.797 1255 210 20 2000 3230 239256319 239255072 0.000000e+00 953.0
17 TraesCS4B01G164100 chr5B 85.119 840 124 1 2392 3230 356217473 356218312 0.000000e+00 857.0
18 TraesCS4B01G164100 chr7A 91.888 641 48 3 1 638 486241091 486240452 0.000000e+00 893.0
19 TraesCS4B01G164100 chr7A 93.478 46 3 0 486 531 516995301 516995346 5.780000e-08 69.4
20 TraesCS4B01G164100 chr2A 91.875 640 49 3 1 638 455465511 455466149 0.000000e+00 891.0
21 TraesCS4B01G164100 chr2A 75.690 580 128 8 1196 1762 732233072 732232493 8.830000e-71 278.0
22 TraesCS4B01G164100 chr2B 90.923 639 57 1 1 638 373269111 373269749 0.000000e+00 857.0
23 TraesCS4B01G164100 chr2B 89.302 645 58 9 1 638 765210520 765211160 0.000000e+00 798.0
24 TraesCS4B01G164100 chr2B 78.871 620 122 8 1501 2116 730031488 730030874 8.340000e-111 411.0
25 TraesCS4B01G164100 chr2B 93.919 148 9 0 2 149 729806566 729806713 1.170000e-54 224.0
26 TraesCS4B01G164100 chr3D 87.618 638 78 1 2 638 318992776 318992139 0.000000e+00 739.0
27 TraesCS4B01G164100 chrUn 79.081 1023 180 16 725 1725 143798038 143799048 0.000000e+00 673.0
28 TraesCS4B01G164100 chrUn 78.261 874 156 16 724 1575 26406381 26405520 6.140000e-147 531.0
29 TraesCS4B01G164100 chrUn 81.116 466 73 4 1122 1575 203671572 203671110 3.060000e-95 359.0
30 TraesCS4B01G164100 chr6B 78.689 122 26 0 3064 3185 163803097 163802976 7.430000e-12 82.4


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 TraesCS4B01G164100 chr4B 339472675 339475904 3229 False 5965.0 5965 100.0000 1 3230 1 chr4B.!!$F1 3229
1 TraesCS4B01G164100 chr6A 2157168 2159678 2510 False 1975.0 1975 81.0280 724 3230 1 chr6A.!!$F1 2506
2 TraesCS4B01G164100 chr6A 39433858 39436306 2448 True 1099.5 1236 83.0195 750 3230 2 chr6A.!!$R1 2480
3 TraesCS4B01G164100 chr1A 527674825 527677344 2519 False 1755.0 1755 79.5370 725 3230 1 chr1A.!!$F1 2505
4 TraesCS4B01G164100 chr1B 379623958 379626468 2510 True 1744.0 1744 79.5440 724 3220 1 chr1B.!!$R2 2496
5 TraesCS4B01G164100 chr1B 480458962 480460658 1696 False 1441.0 1441 82.2010 1543 3230 1 chr1B.!!$F1 1687
6 TraesCS4B01G164100 chr3B 495714019 495716528 2509 True 1712.0 1712 79.2930 725 3230 1 chr3B.!!$R1 2505
7 TraesCS4B01G164100 chr3B 55705903 55706541 638 False 785.0 785 88.8890 1 638 1 chr3B.!!$F1 637
8 TraesCS4B01G164100 chr2D 296705783 296707232 1449 False 1280.0 1280 82.8180 725 2161 1 chr2D.!!$F2 1436
9 TraesCS4B01G164100 chr4A 742975227 742975861 634 False 987.0 987 94.6790 1 638 1 chr4A.!!$F1 637
10 TraesCS4B01G164100 chr4A 478162338 478163501 1163 True 510.0 510 75.1480 801 1947 1 chr4A.!!$R1 1146
11 TraesCS4B01G164100 chr1D 420101548 420102186 638 False 963.0 963 93.8970 1 638 1 chr1D.!!$F1 637
12 TraesCS4B01G164100 chr5B 239255072 239256319 1247 True 953.0 953 80.7970 2000 3230 1 chr5B.!!$R1 1230
13 TraesCS4B01G164100 chr5B 356217473 356218312 839 False 857.0 857 85.1190 2392 3230 1 chr5B.!!$F1 838
14 TraesCS4B01G164100 chr7A 486240452 486241091 639 True 893.0 893 91.8880 1 638 1 chr7A.!!$R1 637
15 TraesCS4B01G164100 chr2A 455465511 455466149 638 False 891.0 891 91.8750 1 638 1 chr2A.!!$F1 637
16 TraesCS4B01G164100 chr2A 732232493 732233072 579 True 278.0 278 75.6900 1196 1762 1 chr2A.!!$R1 566
17 TraesCS4B01G164100 chr2B 373269111 373269749 638 False 857.0 857 90.9230 1 638 1 chr2B.!!$F1 637
18 TraesCS4B01G164100 chr2B 765210520 765211160 640 False 798.0 798 89.3020 1 638 1 chr2B.!!$F3 637
19 TraesCS4B01G164100 chr2B 730030874 730031488 614 True 411.0 411 78.8710 1501 2116 1 chr2B.!!$R1 615
20 TraesCS4B01G164100 chr3D 318992139 318992776 637 True 739.0 739 87.6180 2 638 1 chr3D.!!$R1 636
21 TraesCS4B01G164100 chrUn 143798038 143799048 1010 False 673.0 673 79.0810 725 1725 1 chrUn.!!$F1 1000
22 TraesCS4B01G164100 chrUn 26405520 26406381 861 True 531.0 531 78.2610 724 1575 1 chrUn.!!$R1 851

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
701 708 0.034896 GCTGAGTTTGGAACGGGAGA 59.965 55.0 0.00 0.0 36.23 3.71 F
1773 1823 0.035534 ACAATGCCATCGTGCACCTA 60.036 50.0 12.15 0.0 45.48 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 1977 0.108662 TCGATGATGCACTTGTCGCT 60.109 50.0 0.0 0.0 32.74 4.93 R
2913 2992 0.531753 GCTTTGGAGGAGCGGAGATC 60.532 60.0 0.0 0.0 45.39 2.75 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
47 48 6.195600 TGGGAAACTTACTACCAAGATTGT 57.804 37.500 0.00 0.00 0.00 2.71
50 51 6.371825 GGGAAACTTACTACCAAGATTGTCTG 59.628 42.308 0.00 0.00 0.00 3.51
71 72 1.344114 CCAAGTGACAAAATGGTGGGG 59.656 52.381 0.00 0.00 0.00 4.96
309 310 1.673665 CCACTCTCCCAGCAAGCAC 60.674 63.158 0.00 0.00 0.00 4.40
320 321 3.444742 CCCAGCAAGCACTCAATCAATTA 59.555 43.478 0.00 0.00 0.00 1.40
355 356 7.224753 ACAAGACCAACTTCATAGTATTATGCG 59.775 37.037 0.46 0.00 37.23 4.73
455 456 2.168313 TGACAAGACTGAAGCTCACACA 59.832 45.455 0.00 0.00 0.00 3.72
606 613 2.148768 TGCACTCTGTTCAGATGCAAG 58.851 47.619 23.45 9.51 43.00 4.01
616 623 4.883585 TGTTCAGATGCAAGTCAAGAAACT 59.116 37.500 0.00 0.00 0.00 2.66
638 645 8.924511 AACTTTAATTCATCTCTTCTGGAACA 57.075 30.769 0.00 0.00 0.00 3.18
652 659 3.254470 TGGAACAGAGACACGTTTTGA 57.746 42.857 0.00 0.00 0.00 2.69
653 660 3.194861 TGGAACAGAGACACGTTTTGAG 58.805 45.455 0.00 0.00 0.00 3.02
654 661 3.195661 GGAACAGAGACACGTTTTGAGT 58.804 45.455 0.00 0.00 0.00 3.41
655 662 4.142116 TGGAACAGAGACACGTTTTGAGTA 60.142 41.667 0.00 0.00 0.00 2.59
656 663 4.208666 GGAACAGAGACACGTTTTGAGTAC 59.791 45.833 0.00 0.00 0.00 2.73
657 664 4.650754 ACAGAGACACGTTTTGAGTACT 57.349 40.909 0.00 0.00 0.00 2.73
658 665 5.007385 ACAGAGACACGTTTTGAGTACTT 57.993 39.130 0.00 0.00 0.00 2.24
659 666 5.041940 ACAGAGACACGTTTTGAGTACTTC 58.958 41.667 0.00 0.00 0.00 3.01
660 667 5.041287 CAGAGACACGTTTTGAGTACTTCA 58.959 41.667 0.00 0.00 0.00 3.02
661 668 5.518847 CAGAGACACGTTTTGAGTACTTCAA 59.481 40.000 0.00 0.11 43.92 2.69
672 679 5.689383 TGAGTACTTCAAATCACTTTGCC 57.311 39.130 0.00 0.00 41.29 4.52
673 680 5.376625 TGAGTACTTCAAATCACTTTGCCT 58.623 37.500 0.00 0.00 41.29 4.75
674 681 5.827797 TGAGTACTTCAAATCACTTTGCCTT 59.172 36.000 0.00 0.00 41.29 4.35
675 682 6.076981 AGTACTTCAAATCACTTTGCCTTG 57.923 37.500 0.00 0.00 41.29 3.61
676 683 4.326504 ACTTCAAATCACTTTGCCTTGG 57.673 40.909 0.00 0.00 41.29 3.61
677 684 2.818130 TCAAATCACTTTGCCTTGGC 57.182 45.000 4.43 4.43 41.29 4.52
678 685 2.037901 TCAAATCACTTTGCCTTGGCA 58.962 42.857 10.65 10.65 41.29 4.92
679 686 2.633967 TCAAATCACTTTGCCTTGGCAT 59.366 40.909 15.58 0.00 41.29 4.40
680 687 3.831333 TCAAATCACTTTGCCTTGGCATA 59.169 39.130 15.58 9.78 41.29 3.14
681 688 4.467082 TCAAATCACTTTGCCTTGGCATAT 59.533 37.500 15.58 1.24 41.29 1.78
682 689 4.395959 AATCACTTTGCCTTGGCATATG 57.604 40.909 15.58 13.21 0.00 1.78
683 690 1.477700 TCACTTTGCCTTGGCATATGC 59.522 47.619 19.79 19.79 41.14 3.14
684 691 1.479323 CACTTTGCCTTGGCATATGCT 59.521 47.619 26.12 0.12 41.70 3.79
685 692 1.479323 ACTTTGCCTTGGCATATGCTG 59.521 47.619 26.12 16.08 41.70 4.41
686 693 1.752498 CTTTGCCTTGGCATATGCTGA 59.248 47.619 26.12 14.24 41.70 4.26
687 694 1.395635 TTGCCTTGGCATATGCTGAG 58.604 50.000 26.12 21.50 41.70 3.35
688 695 0.256752 TGCCTTGGCATATGCTGAGT 59.743 50.000 26.12 0.00 41.70 3.41
689 696 1.341285 TGCCTTGGCATATGCTGAGTT 60.341 47.619 26.12 0.00 41.70 3.01
690 697 1.753073 GCCTTGGCATATGCTGAGTTT 59.247 47.619 26.12 0.00 41.70 2.66
691 698 2.480759 GCCTTGGCATATGCTGAGTTTG 60.481 50.000 26.12 12.47 41.70 2.93
692 699 2.100252 CCTTGGCATATGCTGAGTTTGG 59.900 50.000 26.12 14.52 41.70 3.28
693 700 2.804986 TGGCATATGCTGAGTTTGGA 57.195 45.000 26.12 0.00 41.70 3.53
694 701 3.084536 TGGCATATGCTGAGTTTGGAA 57.915 42.857 26.12 0.00 41.70 3.53
695 702 2.754552 TGGCATATGCTGAGTTTGGAAC 59.245 45.455 26.12 6.45 41.70 3.62
696 703 2.223340 GGCATATGCTGAGTTTGGAACG 60.223 50.000 26.12 0.00 41.70 3.95
697 704 2.223340 GCATATGCTGAGTTTGGAACGG 60.223 50.000 20.64 0.00 38.21 4.44
698 705 2.107950 TATGCTGAGTTTGGAACGGG 57.892 50.000 0.00 0.00 36.23 5.28
699 706 0.400213 ATGCTGAGTTTGGAACGGGA 59.600 50.000 0.00 0.00 36.23 5.14
700 707 0.250295 TGCTGAGTTTGGAACGGGAG 60.250 55.000 0.00 0.00 36.23 4.30
701 708 0.034896 GCTGAGTTTGGAACGGGAGA 59.965 55.000 0.00 0.00 36.23 3.71
702 709 1.941668 GCTGAGTTTGGAACGGGAGAG 60.942 57.143 0.00 0.00 36.23 3.20
703 710 0.034896 TGAGTTTGGAACGGGAGAGC 59.965 55.000 0.00 0.00 36.23 4.09
704 711 0.321996 GAGTTTGGAACGGGAGAGCT 59.678 55.000 0.00 0.00 36.23 4.09
705 712 1.549170 GAGTTTGGAACGGGAGAGCTA 59.451 52.381 0.00 0.00 36.23 3.32
706 713 1.550976 AGTTTGGAACGGGAGAGCTAG 59.449 52.381 0.00 0.00 36.23 3.42
707 714 0.249398 TTTGGAACGGGAGAGCTAGC 59.751 55.000 6.62 6.62 0.00 3.42
708 715 1.614241 TTGGAACGGGAGAGCTAGCC 61.614 60.000 12.13 2.81 0.00 3.93
709 716 2.058595 GGAACGGGAGAGCTAGCCA 61.059 63.158 12.13 0.00 0.00 4.75
710 717 1.614241 GGAACGGGAGAGCTAGCCAA 61.614 60.000 12.13 0.00 0.00 4.52
711 718 0.460459 GAACGGGAGAGCTAGCCAAC 60.460 60.000 12.13 3.47 0.00 3.77
712 719 1.900545 AACGGGAGAGCTAGCCAACC 61.901 60.000 12.13 11.82 0.00 3.77
713 720 2.911928 GGGAGAGCTAGCCAACCC 59.088 66.667 19.88 19.88 0.00 4.11
714 721 2.747443 GGGAGAGCTAGCCAACCCC 61.747 68.421 22.41 18.37 0.00 4.95
715 722 2.501610 GAGAGCTAGCCAACCCCG 59.498 66.667 12.13 0.00 0.00 5.73
716 723 3.741830 GAGAGCTAGCCAACCCCGC 62.742 68.421 12.13 0.00 0.00 6.13
717 724 4.858680 GAGCTAGCCAACCCCGCC 62.859 72.222 12.13 0.00 0.00 6.13
774 781 4.776322 CCACCAGATTCCGGCGCA 62.776 66.667 10.83 0.00 0.00 6.09
865 879 1.078848 CAGCCTGCAGGGTAGTGAC 60.079 63.158 35.65 16.26 45.47 3.67
892 906 4.051167 CAGCCATCCCCAGTGCCA 62.051 66.667 0.00 0.00 0.00 4.92
906 920 1.701847 AGTGCCAGACTTGGTCAGATT 59.298 47.619 0.52 0.00 46.80 2.40
940 954 0.803740 AGGTGTCGTTCTCTCTACGC 59.196 55.000 0.00 0.00 38.81 4.42
969 983 1.863662 GCGTCAACGACCCTCTCTGA 61.864 60.000 6.75 0.00 43.02 3.27
971 993 0.959553 GTCAACGACCCTCTCTGACA 59.040 55.000 0.00 0.00 37.07 3.58
980 1002 1.827969 CCCTCTCTGACACGAATCCTT 59.172 52.381 0.00 0.00 0.00 3.36
1007 1029 2.352422 GAGTGCTCCCATGCCACA 59.648 61.111 0.00 0.00 0.00 4.17
1013 1035 3.610619 CTCCCATGCCACAGACGCA 62.611 63.158 0.00 0.00 41.28 5.24
1023 1045 0.036952 CACAGACGCATTCTCCACCT 60.037 55.000 0.00 0.00 28.96 4.00
1030 1052 1.890894 CATTCTCCACCTCGGTCGT 59.109 57.895 0.00 0.00 35.57 4.34
1074 1099 2.540515 CTGCGACTTATGTCCATCGTT 58.459 47.619 3.35 0.00 39.94 3.85
1124 1149 1.224315 CTTCGGGGCATGGTGATGA 59.776 57.895 0.00 0.00 0.00 2.92
1162 1187 3.929948 GCAAAGATCGCCGGCTCG 61.930 66.667 26.68 10.37 0.00 5.03
1330 1355 4.466726 GTGTAGACTGTAGGGATCCAGTTT 59.533 45.833 15.23 6.17 41.80 2.66
1331 1356 4.466370 TGTAGACTGTAGGGATCCAGTTTG 59.534 45.833 15.23 2.93 41.80 2.93
1341 1366 1.945394 GATCCAGTTTGCTGCATCGAT 59.055 47.619 1.84 0.00 41.26 3.59
1361 1386 0.459489 TGCAAACTTCAAGGCCACAC 59.541 50.000 5.01 0.00 0.00 3.82
1411 1461 4.379243 CTCCTGTGAAGGCGCGGT 62.379 66.667 8.83 0.00 0.00 5.68
1446 1496 2.509336 CGTGGCCCGATCTGTGAC 60.509 66.667 0.00 0.00 39.56 3.67
1581 1631 1.847328 TGGAGCGTCAGATGTTCCTA 58.153 50.000 22.36 9.46 0.00 2.94
1585 1635 2.685897 GAGCGTCAGATGTTCCTACTCT 59.314 50.000 0.00 0.00 0.00 3.24
1608 1658 2.412323 CCATGCGGTGCTGCTGATT 61.412 57.895 0.00 0.00 35.36 2.57
1742 1792 0.457851 CTCGTCCATTTCGAGCTCCT 59.542 55.000 8.47 0.00 45.77 3.69
1760 1810 1.005294 CTGGCGCACAAAGACAATGC 61.005 55.000 10.83 0.00 35.96 3.56
1761 1811 1.734117 GGCGCACAAAGACAATGCC 60.734 57.895 10.83 0.00 35.91 4.40
1762 1812 1.007502 GCGCACAAAGACAATGCCA 60.008 52.632 0.30 0.00 35.91 4.92
1773 1823 0.035534 ACAATGCCATCGTGCACCTA 60.036 50.000 12.15 0.00 45.48 3.08
1834 1884 3.681835 GGCACGAGGACGACCACT 61.682 66.667 6.71 0.00 42.66 4.00
1842 1892 0.108585 AGGACGACCACTTTGTGCAT 59.891 50.000 6.71 0.00 38.94 3.96
1851 1901 2.624838 CCACTTTGTGCATCAGGAGTTT 59.375 45.455 0.00 0.00 31.34 2.66
1868 1918 1.527311 GTTTCTTCTCCACGTCTGCAC 59.473 52.381 0.00 0.00 0.00 4.57
1896 1946 1.078143 GAAGATGCCGCTCCACCTT 60.078 57.895 0.00 0.00 0.00 3.50
1908 1958 2.487265 GCTCCACCTTTGGTCTCTTGAA 60.487 50.000 0.00 0.00 44.35 2.69
1964 2014 1.303888 ACCGCCTCGACAGTAGGAA 60.304 57.895 0.00 0.00 36.08 3.36
1974 2024 1.177256 ACAGTAGGAACCACGAGCGT 61.177 55.000 0.00 0.00 0.00 5.07
1998 2048 2.233271 CACCTGAAGACCTTTGCATGT 58.767 47.619 0.00 0.00 0.00 3.21
2188 2254 4.057428 GACTGGTCACCGCGCTCT 62.057 66.667 5.56 0.00 0.00 4.09
2230 2296 1.118965 TGCCCTTGTCGGAGTCTGAA 61.119 55.000 2.39 0.00 33.16 3.02
2272 2338 4.402528 TGGCCGGGAACATGGACG 62.403 66.667 2.18 0.00 36.07 4.79
2322 2388 3.246112 CCACCCGACCCTGTTGGA 61.246 66.667 1.92 0.00 39.36 3.53
2329 2395 0.833287 CGACCCTGTTGGATCCATCT 59.167 55.000 17.06 0.00 38.00 2.90
2701 2773 1.812922 GCTGCCTCGTGTGGATGAG 60.813 63.158 0.00 0.00 35.26 2.90
2733 2805 1.667154 CTCGAGGAGTCCATCGCCAA 61.667 60.000 19.94 7.87 38.50 4.52
2823 2896 1.603842 CCAGACCAGCCTGCATGTA 59.396 57.895 0.00 0.00 32.97 2.29
2826 2899 0.911525 AGACCAGCCTGCATGTAGGT 60.912 55.000 27.95 11.62 40.11 3.08
2837 2910 1.521457 ATGTAGGTGCCATGACGCG 60.521 57.895 3.53 3.53 0.00 6.01
2850 2923 0.670239 TGACGCGACAAGTCATGCAT 60.670 50.000 15.93 0.00 42.91 3.96
2866 2939 1.730501 GCATCTGCAGCTCAACAGTA 58.269 50.000 9.47 0.00 41.59 2.74
2902 2981 1.429825 CGCCTCTTCGTCGATGTCT 59.570 57.895 4.21 0.00 0.00 3.41
2913 2992 2.786495 CGATGTCTCCCCTCCCGTG 61.786 68.421 0.00 0.00 0.00 4.94
2925 3004 2.835431 CCCGTGATCTCCGCTCCT 60.835 66.667 0.00 0.00 0.00 3.69
2930 3009 0.537188 GTGATCTCCGCTCCTCCAAA 59.463 55.000 0.00 0.00 0.00 3.28
2955 3037 3.551496 CTCCGCTGCACCTCCCAAA 62.551 63.158 0.00 0.00 0.00 3.28
2962 3044 0.482446 TGCACCTCCCAAAACCAGAT 59.518 50.000 0.00 0.00 0.00 2.90
2966 3048 2.003072 ACCTCCCAAAACCAGATCCAT 58.997 47.619 0.00 0.00 0.00 3.41
2975 3057 0.030297 ACCAGATCCATCTCTGCCCT 60.030 55.000 0.00 0.00 41.12 5.19
3062 3144 4.373116 GGTGGTCAAGCGCCTCGA 62.373 66.667 2.29 0.00 0.00 4.04
3089 3171 1.916181 GGGACCCAAGGAGAAGATGAA 59.084 52.381 5.33 0.00 0.00 2.57
3098 3180 4.313020 AGGAGAAGATGAATGCAAAGGT 57.687 40.909 0.00 0.00 0.00 3.50
3100 3182 3.760684 GGAGAAGATGAATGCAAAGGTGT 59.239 43.478 0.00 0.00 0.00 4.16
3111 3193 2.225467 GCAAAGGTGTCTGAAGCTCTT 58.775 47.619 0.00 0.00 0.00 2.85
3115 3197 5.048434 GCAAAGGTGTCTGAAGCTCTTATTT 60.048 40.000 0.00 0.00 0.00 1.40
3135 3217 2.202388 CGTTTCGACGAGCCGCTA 60.202 61.111 0.00 0.00 34.64 4.26
3137 3219 1.138047 CGTTTCGACGAGCCGCTAAT 61.138 55.000 0.00 0.00 34.64 1.73
3171 3253 0.745486 CCATCATCGCCAAGCTCACA 60.745 55.000 0.00 0.00 0.00 3.58
3172 3254 1.306148 CATCATCGCCAAGCTCACAT 58.694 50.000 0.00 0.00 0.00 3.21
3185 3267 4.082523 CACATGCCTCGACCCGGT 62.083 66.667 0.00 0.00 0.00 5.28
3186 3268 2.363276 ACATGCCTCGACCCGGTA 60.363 61.111 0.00 0.00 0.00 4.02
3201 3283 2.190578 GTAGCCCTCCGCATTGCT 59.809 61.111 7.12 0.00 41.38 3.91
3205 3287 2.825836 CCCTCCGCATTGCTGGTC 60.826 66.667 15.72 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.361757 CACCATTTTGTCACTTGGCAGA 59.638 45.455 0.00 0.00 32.26 4.26
50 51 1.270252 CCCACCATTTTGTCACTTGGC 60.270 52.381 0.00 0.00 32.26 4.52
71 72 4.407296 AGAATACCTCTCCACCAGAATGAC 59.593 45.833 0.00 0.00 39.69 3.06
139 140 2.127708 ACAGAGTGGTGTCTCCCTTTT 58.872 47.619 0.00 0.00 35.28 2.27
186 187 3.492102 AGGTAGCTTTTGTTGCAGAGA 57.508 42.857 0.00 0.00 0.00 3.10
309 310 8.669243 GTCTTGTAGGAGGTTTAATTGATTGAG 58.331 37.037 0.00 0.00 0.00 3.02
320 321 4.165372 TGAAGTTGGTCTTGTAGGAGGTTT 59.835 41.667 0.00 0.00 36.40 3.27
355 356 3.594134 CATTGGTCTGTCTCTTCAGTCC 58.406 50.000 0.00 0.00 41.54 3.85
455 456 5.184892 ACTTCCATAACTGCCTGAAGATT 57.815 39.130 0.00 0.00 36.72 2.40
616 623 8.597167 TCTCTGTTCCAGAAGAGATGAATTAAA 58.403 33.333 7.61 0.00 43.09 1.52
638 645 5.258456 TGAAGTACTCAAAACGTGTCTCT 57.742 39.130 0.00 0.00 0.00 3.10
639 646 5.961395 TTGAAGTACTCAAAACGTGTCTC 57.039 39.130 0.00 0.00 41.21 3.36
649 656 5.827797 AGGCAAAGTGATTTGAAGTACTCAA 59.172 36.000 0.00 0.00 42.48 3.02
650 657 5.376625 AGGCAAAGTGATTTGAAGTACTCA 58.623 37.500 0.00 0.00 33.95 3.41
651 658 5.948992 AGGCAAAGTGATTTGAAGTACTC 57.051 39.130 0.00 0.00 33.95 2.59
652 659 5.010012 CCAAGGCAAAGTGATTTGAAGTACT 59.990 40.000 4.96 0.00 33.95 2.73
653 660 5.222631 CCAAGGCAAAGTGATTTGAAGTAC 58.777 41.667 4.96 0.00 33.95 2.73
654 661 4.261994 GCCAAGGCAAAGTGATTTGAAGTA 60.262 41.667 6.14 0.00 41.49 2.24
655 662 3.493176 GCCAAGGCAAAGTGATTTGAAGT 60.493 43.478 6.14 0.00 41.49 3.01
656 663 3.062042 GCCAAGGCAAAGTGATTTGAAG 58.938 45.455 6.14 0.00 41.49 3.02
657 664 3.110447 GCCAAGGCAAAGTGATTTGAA 57.890 42.857 6.14 0.00 41.49 2.69
658 665 2.818130 GCCAAGGCAAAGTGATTTGA 57.182 45.000 6.14 0.00 41.49 2.69
670 677 1.396653 AACTCAGCATATGCCAAGGC 58.603 50.000 23.96 3.61 43.38 4.35
671 678 2.100252 CCAAACTCAGCATATGCCAAGG 59.900 50.000 23.96 13.76 43.38 3.61
672 679 3.018856 TCCAAACTCAGCATATGCCAAG 58.981 45.455 23.96 21.66 43.38 3.61
673 680 3.084536 TCCAAACTCAGCATATGCCAA 57.915 42.857 23.96 11.44 43.38 4.52
674 681 2.754552 GTTCCAAACTCAGCATATGCCA 59.245 45.455 23.96 10.28 43.38 4.92
675 682 2.223340 CGTTCCAAACTCAGCATATGCC 60.223 50.000 23.96 6.56 43.38 4.40
676 683 2.223340 CCGTTCCAAACTCAGCATATGC 60.223 50.000 20.36 20.36 42.49 3.14
677 684 2.355756 CCCGTTCCAAACTCAGCATATG 59.644 50.000 0.00 0.00 0.00 1.78
678 685 2.238646 TCCCGTTCCAAACTCAGCATAT 59.761 45.455 0.00 0.00 0.00 1.78
679 686 1.626321 TCCCGTTCCAAACTCAGCATA 59.374 47.619 0.00 0.00 0.00 3.14
680 687 0.400213 TCCCGTTCCAAACTCAGCAT 59.600 50.000 0.00 0.00 0.00 3.79
681 688 0.250295 CTCCCGTTCCAAACTCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
682 689 0.034896 TCTCCCGTTCCAAACTCAGC 59.965 55.000 0.00 0.00 0.00 4.26
683 690 1.941668 GCTCTCCCGTTCCAAACTCAG 60.942 57.143 0.00 0.00 0.00 3.35
684 691 0.034896 GCTCTCCCGTTCCAAACTCA 59.965 55.000 0.00 0.00 0.00 3.41
685 692 0.321996 AGCTCTCCCGTTCCAAACTC 59.678 55.000 0.00 0.00 0.00 3.01
686 693 1.550976 CTAGCTCTCCCGTTCCAAACT 59.449 52.381 0.00 0.00 0.00 2.66
687 694 2.007547 GCTAGCTCTCCCGTTCCAAAC 61.008 57.143 7.70 0.00 0.00 2.93
688 695 0.249398 GCTAGCTCTCCCGTTCCAAA 59.751 55.000 7.70 0.00 0.00 3.28
689 696 1.614241 GGCTAGCTCTCCCGTTCCAA 61.614 60.000 15.72 0.00 0.00 3.53
690 697 2.058595 GGCTAGCTCTCCCGTTCCA 61.059 63.158 15.72 0.00 0.00 3.53
691 698 1.614241 TTGGCTAGCTCTCCCGTTCC 61.614 60.000 15.72 0.00 0.00 3.62
692 699 0.460459 GTTGGCTAGCTCTCCCGTTC 60.460 60.000 15.72 0.00 0.00 3.95
693 700 1.597461 GTTGGCTAGCTCTCCCGTT 59.403 57.895 15.72 0.00 0.00 4.44
694 701 2.359967 GGTTGGCTAGCTCTCCCGT 61.360 63.158 15.72 0.00 0.00 5.28
695 702 2.501610 GGTTGGCTAGCTCTCCCG 59.498 66.667 15.72 0.00 0.00 5.14
696 703 2.747443 GGGGTTGGCTAGCTCTCCC 61.747 68.421 23.47 23.47 34.68 4.30
697 704 2.911928 GGGGTTGGCTAGCTCTCC 59.088 66.667 15.72 13.41 0.00 3.71
698 705 2.501610 CGGGGTTGGCTAGCTCTC 59.498 66.667 15.72 5.60 0.00 3.20
699 706 3.787001 GCGGGGTTGGCTAGCTCT 61.787 66.667 15.72 0.00 0.00 4.09
700 707 4.858680 GGCGGGGTTGGCTAGCTC 62.859 72.222 15.72 5.44 0.00 4.09
756 763 4.778143 GCGCCGGAATCTGGTGGT 62.778 66.667 21.84 0.00 37.47 4.16
815 825 1.626356 CCAAAGGATCGAGGGGAGCA 61.626 60.000 0.00 0.00 30.89 4.26
880 894 1.687612 CAAGTCTGGCACTGGGGAT 59.312 57.895 0.00 0.00 34.56 3.85
881 895 2.528818 CCAAGTCTGGCACTGGGGA 61.529 63.158 0.00 0.00 42.32 4.81
892 906 1.066573 CCGCTGAATCTGACCAAGTCT 60.067 52.381 0.00 0.00 33.15 3.24
959 973 1.187087 GGATTCGTGTCAGAGAGGGT 58.813 55.000 0.00 0.00 0.00 4.34
1007 1029 1.513158 CGAGGTGGAGAATGCGTCT 59.487 57.895 0.00 0.00 40.25 4.18
1013 1035 0.246635 CAACGACCGAGGTGGAGAAT 59.753 55.000 11.22 0.00 42.00 2.40
1023 1045 4.980805 GGGCTGCACAACGACCGA 62.981 66.667 0.50 0.00 0.00 4.69
1055 1080 2.267426 CAACGATGGACATAAGTCGCA 58.733 47.619 0.00 0.00 45.92 5.10
1059 1084 3.259064 CCGAACAACGATGGACATAAGT 58.741 45.455 0.00 0.00 45.77 2.24
1064 1089 1.669760 GGCCGAACAACGATGGACA 60.670 57.895 0.00 0.00 45.77 4.02
1074 1099 3.646715 CAGGGGAAGGGCCGAACA 61.647 66.667 0.00 0.00 37.63 3.18
1341 1366 1.134848 GTGTGGCCTTGAAGTTTGCAA 60.135 47.619 3.32 0.00 0.00 4.08
1352 1377 1.421646 AGTCTTTGCTAGTGTGGCCTT 59.578 47.619 3.32 0.00 0.00 4.35
1438 1488 0.615331 AAGCGGATGTGGTCACAGAT 59.385 50.000 9.72 0.00 45.48 2.90
1446 1496 2.190578 GAGGGGAAGCGGATGTGG 59.809 66.667 0.00 0.00 0.00 4.17
1568 1618 3.732471 GCGACAGAGTAGGAACATCTGAC 60.732 52.174 8.32 1.67 42.48 3.51
1608 1658 2.377810 ATGGCGCTCCTCCATGGAA 61.378 57.895 17.00 0.10 45.63 3.53
1710 1760 0.822164 GGACGAGAAAATCCTCCGGA 59.178 55.000 2.93 2.93 35.55 5.14
1740 1790 0.387622 CATTGTCTTTGTGCGCCAGG 60.388 55.000 4.18 0.10 0.00 4.45
1742 1792 1.007502 GCATTGTCTTTGTGCGCCA 60.008 52.632 4.18 0.00 0.00 5.69
1760 1810 1.227380 GAGCCTAGGTGCACGATGG 60.227 63.158 11.45 12.95 0.00 3.51
1761 1811 1.227380 GGAGCCTAGGTGCACGATG 60.227 63.158 11.45 2.67 0.00 3.84
1762 1812 1.050988 ATGGAGCCTAGGTGCACGAT 61.051 55.000 11.45 4.46 33.77 3.73
1773 1823 1.215647 GTCGACGTTGATGGAGCCT 59.784 57.895 9.14 0.00 0.00 4.58
1834 1884 4.464008 AGAAGAAACTCCTGATGCACAAA 58.536 39.130 0.00 0.00 0.00 2.83
1851 1901 1.666011 GGTGCAGACGTGGAGAAGA 59.334 57.895 0.00 0.00 0.00 2.87
1896 1946 1.374947 CGCCCCTTCAAGAGACCAA 59.625 57.895 0.00 0.00 0.00 3.67
1927 1977 0.108662 TCGATGATGCACTTGTCGCT 60.109 50.000 0.00 0.00 32.74 4.93
1974 2024 0.178992 CAAAGGTCTTCAGGTGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
1981 2031 2.029649 CCCAACATGCAAAGGTCTTCAG 60.030 50.000 0.00 0.00 0.00 3.02
1998 2048 2.088096 ATCCCACACCCACACCCAA 61.088 57.895 0.00 0.00 0.00 4.12
2132 2189 2.202743 GAGCATGTCGTGGCGCTA 60.203 61.111 7.64 0.00 34.12 4.26
2217 2283 0.889638 AGCGTCTTCAGACTCCGACA 60.890 55.000 5.44 0.00 42.66 4.35
2303 2369 4.263572 CAACAGGGTCGGGTGGCA 62.264 66.667 0.00 0.00 0.00 4.92
2312 2378 0.921896 CCAGATGGATCCAACAGGGT 59.078 55.000 20.67 0.00 35.97 4.34
2318 2384 1.153107 CGCAGCCAGATGGATCCAA 60.153 57.895 20.67 1.96 37.39 3.53
2322 2388 3.769369 CTGCCGCAGCCAGATGGAT 62.769 63.158 7.61 0.00 38.69 3.41
2464 2536 2.125391 CGGCTTGAGCTAGCAGCA 60.125 61.111 22.64 15.23 45.56 4.41
2682 2754 2.046988 CATCCACACGAGGCAGCA 60.047 61.111 0.00 0.00 0.00 4.41
2719 2791 3.195698 GCGTTGGCGATGGACTCC 61.196 66.667 0.00 0.00 41.33 3.85
2823 2896 3.529341 TTGTCGCGTCATGGCACCT 62.529 57.895 6.92 0.00 0.00 4.00
2826 2899 2.027073 GACTTGTCGCGTCATGGCA 61.027 57.895 17.72 0.00 0.00 4.92
2850 2923 1.047801 TGGTACTGTTGAGCTGCAGA 58.952 50.000 20.43 0.00 36.62 4.26
2902 2981 2.282446 GGAGATCACGGGAGGGGA 59.718 66.667 0.00 0.00 0.00 4.81
2913 2992 0.531753 GCTTTGGAGGAGCGGAGATC 60.532 60.000 0.00 0.00 45.39 2.75
2949 3028 3.054139 CAGAGATGGATCTGGTTTTGGGA 60.054 47.826 0.00 0.00 42.52 4.37
2955 3037 0.842635 GGGCAGAGATGGATCTGGTT 59.157 55.000 5.92 0.00 45.66 3.67
2962 3044 1.412217 CCTGACTAGGGCAGAGATGGA 60.412 57.143 14.37 0.00 40.63 3.41
2975 3057 3.118454 GCGCGCTTTGCCTGACTA 61.118 61.111 26.67 0.00 42.08 2.59
3062 3144 1.852157 TCCTTGGGTCCCAGCATGT 60.852 57.895 11.40 0.00 33.81 3.21
3089 3171 2.157738 GAGCTTCAGACACCTTTGCAT 58.842 47.619 0.00 0.00 0.00 3.96
3098 3180 3.002791 CGGCAAATAAGAGCTTCAGACA 58.997 45.455 0.00 0.00 0.00 3.41
3100 3182 3.334583 ACGGCAAATAAGAGCTTCAGA 57.665 42.857 0.00 0.00 0.00 3.27
3135 3217 4.042884 TGATGGAGATGTCCTCTTCCATT 58.957 43.478 10.72 0.00 44.30 3.16
3137 3219 3.120468 TGATGGAGATGTCCTCTTCCA 57.880 47.619 10.72 0.00 44.30 3.53
3171 3253 3.537874 GCTACCGGGTCGAGGCAT 61.538 66.667 6.32 0.00 0.00 4.40
3185 3267 2.190313 CAGCAATGCGGAGGGCTA 59.810 61.111 0.00 0.00 44.05 3.93
3186 3268 4.809496 CCAGCAATGCGGAGGGCT 62.809 66.667 7.00 0.00 44.05 5.19


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

AutoCloner maintained by Alex Coulton.