Multiple sequence alignment - TraesCS7B01G327400

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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 TraesCS7B01G327400 chr7B 100.000 3047 0 0 1 3047 581375261 581372215 0.000000e+00 5627.0
1 TraesCS7B01G327400 chr7B 78.812 505 89 17 1076 1573 580885613 580885120 1.050000e-84 324.0
2 TraesCS7B01G327400 chr7B 78.161 522 84 27 1074 1572 581894373 581893859 3.820000e-79 305.0
3 TraesCS7B01G327400 chr7B 77.589 531 99 16 1055 1576 580970272 580969753 1.370000e-78 303.0
4 TraesCS7B01G327400 chr7D 92.239 2113 102 28 110 2191 538819742 538817661 0.000000e+00 2937.0
5 TraesCS7B01G327400 chr7D 81.637 855 127 20 2193 3047 524919499 524920323 0.000000e+00 682.0
6 TraesCS7B01G327400 chr7D 80.541 740 92 29 2308 3047 539749598 539750285 3.480000e-144 521.0
7 TraesCS7B01G327400 chr7D 79.919 742 119 14 2252 2981 627058530 627057807 4.500000e-143 518.0
8 TraesCS7B01G327400 chr7D 81.308 214 37 3 1074 1285 539134505 539134293 1.450000e-38 171.0
9 TraesCS7B01G327400 chr7A 91.833 1555 46 31 680 2191 620371573 620370057 0.000000e+00 2093.0
10 TraesCS7B01G327400 chr7A 92.727 1375 50 15 725 2075 620486787 620488135 0.000000e+00 1940.0
11 TraesCS7B01G327400 chr7A 80.305 853 140 21 2214 3047 3404428 3403585 1.200000e-173 619.0
12 TraesCS7B01G327400 chr7A 83.398 518 54 20 110 613 620426342 620426841 4.630000e-123 451.0
13 TraesCS7B01G327400 chr7A 78.698 507 88 16 1076 1573 619166916 619166421 1.360000e-83 320.0
14 TraesCS7B01G327400 chr7A 85.388 219 31 1 1358 1576 619576322 619576105 3.060000e-55 226.0
15 TraesCS7B01G327400 chr7A 85.586 222 25 7 1354 1572 620750089 620749872 3.060000e-55 226.0
16 TraesCS7B01G327400 chr7A 96.552 58 2 0 677 734 620426878 620426935 2.500000e-16 97.1
17 TraesCS7B01G327400 chr1D 84.094 855 127 4 2193 3047 341180591 341181436 0.000000e+00 817.0
18 TraesCS7B01G327400 chr1D 80.839 548 76 11 2501 3046 194218550 194219070 1.320000e-108 403.0
19 TraesCS7B01G327400 chr3D 82.147 857 117 18 2193 3047 103234554 103235376 0.000000e+00 702.0
20 TraesCS7B01G327400 chr3D 78.196 876 131 41 2192 3047 596698410 596697575 3.510000e-139 505.0
21 TraesCS7B01G327400 chr2D 82.268 829 122 17 2236 3047 559121179 559121999 0.000000e+00 693.0
22 TraesCS7B01G327400 chr2D 81.274 785 98 24 2266 3047 301528808 301528070 9.410000e-165 590.0
23 TraesCS7B01G327400 chr3B 80.946 803 107 22 2256 3047 28000139 28000906 7.270000e-166 593.0
24 TraesCS7B01G327400 chr3B 82.090 134 19 4 2211 2344 725561412 725561540 3.210000e-20 110.0
25 TraesCS7B01G327400 chr1A 82.043 607 95 9 2442 3047 555611563 555610970 3.510000e-139 505.0
26 TraesCS7B01G327400 chr6D 81.507 584 98 6 2446 3029 275941967 275942540 3.560000e-129 472.0
27 TraesCS7B01G327400 chr5A 77.053 889 142 43 2193 3047 436908117 436907257 3.580000e-124 455.0
28 TraesCS7B01G327400 chr5D 76.497 885 143 45 2195 3046 564448130 564447278 3.630000e-114 422.0
29 TraesCS7B01G327400 chr5D 75.083 903 148 53 2194 3047 36482722 36483596 1.740000e-92 350.0
30 TraesCS7B01G327400 chr5D 76.994 652 103 34 2281 2907 456600177 456600806 2.260000e-86 329.0
31 TraesCS7B01G327400 chr3A 76.771 861 135 42 2193 3040 645701449 645700641 3.630000e-114 422.0
32 TraesCS7B01G327400 chr5B 82.906 351 54 5 2281 2628 681624877 681624530 8.200000e-81 311.0
33 TraesCS7B01G327400 chr4D 97.222 36 1 0 1661 1696 390599781 390599816 9.120000e-06 62.1
34 TraesCS7B01G327400 chr4A 97.222 36 1 0 1661 1696 72296085 72296120 9.120000e-06 62.1
35 TraesCS7B01G327400 chr4B 97.143 35 1 0 1662 1696 480592554 480592588 3.280000e-05 60.2
36 TraesCS7B01G327400 chr6A 85.455 55 8 0 2195 2249 9295403 9295349 1.180000e-04 58.4
37 TraesCS7B01G327400 chr6A 85.455 55 8 0 2195 2249 9300964 9300910 1.180000e-04 58.4


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 TraesCS7B01G327400 chr7B 581372215 581375261 3046 True 5627.00 5627 100.000 1 3047 1 chr7B.!!$R3 3046
1 TraesCS7B01G327400 chr7B 581893859 581894373 514 True 305.00 305 78.161 1074 1572 1 chr7B.!!$R4 498
2 TraesCS7B01G327400 chr7B 580969753 580970272 519 True 303.00 303 77.589 1055 1576 1 chr7B.!!$R2 521
3 TraesCS7B01G327400 chr7D 538817661 538819742 2081 True 2937.00 2937 92.239 110 2191 1 chr7D.!!$R1 2081
4 TraesCS7B01G327400 chr7D 524919499 524920323 824 False 682.00 682 81.637 2193 3047 1 chr7D.!!$F1 854
5 TraesCS7B01G327400 chr7D 539749598 539750285 687 False 521.00 521 80.541 2308 3047 1 chr7D.!!$F2 739
6 TraesCS7B01G327400 chr7D 627057807 627058530 723 True 518.00 518 79.919 2252 2981 1 chr7D.!!$R3 729
7 TraesCS7B01G327400 chr7A 620370057 620371573 1516 True 2093.00 2093 91.833 680 2191 1 chr7A.!!$R4 1511
8 TraesCS7B01G327400 chr7A 620486787 620488135 1348 False 1940.00 1940 92.727 725 2075 1 chr7A.!!$F1 1350
9 TraesCS7B01G327400 chr7A 3403585 3404428 843 True 619.00 619 80.305 2214 3047 1 chr7A.!!$R1 833
10 TraesCS7B01G327400 chr7A 620426342 620426935 593 False 274.05 451 89.975 110 734 2 chr7A.!!$F2 624
11 TraesCS7B01G327400 chr1D 341180591 341181436 845 False 817.00 817 84.094 2193 3047 1 chr1D.!!$F2 854
12 TraesCS7B01G327400 chr1D 194218550 194219070 520 False 403.00 403 80.839 2501 3046 1 chr1D.!!$F1 545
13 TraesCS7B01G327400 chr3D 103234554 103235376 822 False 702.00 702 82.147 2193 3047 1 chr3D.!!$F1 854
14 TraesCS7B01G327400 chr3D 596697575 596698410 835 True 505.00 505 78.196 2192 3047 1 chr3D.!!$R1 855
15 TraesCS7B01G327400 chr2D 559121179 559121999 820 False 693.00 693 82.268 2236 3047 1 chr2D.!!$F1 811
16 TraesCS7B01G327400 chr2D 301528070 301528808 738 True 590.00 590 81.274 2266 3047 1 chr2D.!!$R1 781
17 TraesCS7B01G327400 chr3B 28000139 28000906 767 False 593.00 593 80.946 2256 3047 1 chr3B.!!$F1 791
18 TraesCS7B01G327400 chr1A 555610970 555611563 593 True 505.00 505 82.043 2442 3047 1 chr1A.!!$R1 605
19 TraesCS7B01G327400 chr6D 275941967 275942540 573 False 472.00 472 81.507 2446 3029 1 chr6D.!!$F1 583
20 TraesCS7B01G327400 chr5A 436907257 436908117 860 True 455.00 455 77.053 2193 3047 1 chr5A.!!$R1 854
21 TraesCS7B01G327400 chr5D 564447278 564448130 852 True 422.00 422 76.497 2195 3046 1 chr5D.!!$R1 851
22 TraesCS7B01G327400 chr5D 36482722 36483596 874 False 350.00 350 75.083 2194 3047 1 chr5D.!!$F1 853
23 TraesCS7B01G327400 chr5D 456600177 456600806 629 False 329.00 329 76.994 2281 2907 1 chr5D.!!$F2 626
24 TraesCS7B01G327400 chr3A 645700641 645701449 808 True 422.00 422 76.771 2193 3040 1 chr3A.!!$R1 847

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
573 597 0.036577 ATGCAGTGAGCCAGTGAGTC 60.037 55.0 12.53 0.00 44.83 3.36 F
1650 1776 0.179702 AGATCTCATGCATGCACCGT 59.820 50.0 25.37 4.03 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1779 0.179073 CGTAGAACCTGCATGGGGAG 60.179 60.0 0.0 0.0 41.11 4.3 R
2704 2954 0.325203 AGGAGGAGAAGGGAGAGCAC 60.325 60.0 0.0 0.0 0.00 4.4 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
17 18 4.147587 AGCCCCCATGCCATCACC 62.148 66.667 0.00 0.00 0.00 4.02
22 23 4.854924 CCATGCCATCACCGCCGA 62.855 66.667 0.00 0.00 0.00 5.54
23 24 3.576356 CATGCCATCACCGCCGAC 61.576 66.667 0.00 0.00 0.00 4.79
24 25 3.785859 ATGCCATCACCGCCGACT 61.786 61.111 0.00 0.00 0.00 4.18
25 26 3.329542 ATGCCATCACCGCCGACTT 62.330 57.895 0.00 0.00 0.00 3.01
26 27 3.195698 GCCATCACCGCCGACTTC 61.196 66.667 0.00 0.00 0.00 3.01
27 28 2.511600 CCATCACCGCCGACTTCC 60.512 66.667 0.00 0.00 0.00 3.46
28 29 2.264480 CATCACCGCCGACTTCCA 59.736 61.111 0.00 0.00 0.00 3.53
29 30 2.100631 CATCACCGCCGACTTCCAC 61.101 63.158 0.00 0.00 0.00 4.02
30 31 3.310860 ATCACCGCCGACTTCCACC 62.311 63.158 0.00 0.00 0.00 4.61
36 37 4.096003 CCGACTTCCACCGGGCAT 62.096 66.667 6.32 0.00 41.89 4.40
37 38 2.511600 CGACTTCCACCGGGCATC 60.512 66.667 6.32 0.00 0.00 3.91
38 39 2.668632 GACTTCCACCGGGCATCA 59.331 61.111 6.32 0.00 0.00 3.07
39 40 1.745489 GACTTCCACCGGGCATCAC 60.745 63.158 6.32 0.00 0.00 3.06
40 41 2.185310 GACTTCCACCGGGCATCACT 62.185 60.000 6.32 0.00 0.00 3.41
41 42 1.746615 CTTCCACCGGGCATCACTG 60.747 63.158 6.32 0.00 0.00 3.66
50 51 3.364441 GCATCACTGCCGCCACAA 61.364 61.111 0.00 0.00 42.88 3.33
51 52 2.562912 CATCACTGCCGCCACAAC 59.437 61.111 0.00 0.00 0.00 3.32
52 53 3.049674 ATCACTGCCGCCACAACG 61.050 61.111 0.00 0.00 0.00 4.10
59 60 3.669344 CCGCCACAACGCACCATT 61.669 61.111 0.00 0.00 0.00 3.16
60 61 2.126888 CGCCACAACGCACCATTC 60.127 61.111 0.00 0.00 0.00 2.67
61 62 2.616330 CGCCACAACGCACCATTCT 61.616 57.895 0.00 0.00 0.00 2.40
62 63 1.210155 GCCACAACGCACCATTCTC 59.790 57.895 0.00 0.00 0.00 2.87
63 64 1.875963 CCACAACGCACCATTCTCC 59.124 57.895 0.00 0.00 0.00 3.71
64 65 0.606401 CCACAACGCACCATTCTCCT 60.606 55.000 0.00 0.00 0.00 3.69
65 66 0.518636 CACAACGCACCATTCTCCTG 59.481 55.000 0.00 0.00 0.00 3.86
66 67 1.237285 ACAACGCACCATTCTCCTGC 61.237 55.000 0.00 0.00 0.00 4.85
67 68 1.675641 AACGCACCATTCTCCTGCC 60.676 57.895 0.00 0.00 0.00 4.85
68 69 3.197790 CGCACCATTCTCCTGCCG 61.198 66.667 0.00 0.00 0.00 5.69
69 70 3.512516 GCACCATTCTCCTGCCGC 61.513 66.667 0.00 0.00 0.00 6.53
70 71 2.825836 CACCATTCTCCTGCCGCC 60.826 66.667 0.00 0.00 0.00 6.13
71 72 4.115199 ACCATTCTCCTGCCGCCC 62.115 66.667 0.00 0.00 0.00 6.13
72 73 4.113815 CCATTCTCCTGCCGCCCA 62.114 66.667 0.00 0.00 0.00 5.36
73 74 2.825836 CATTCTCCTGCCGCCCAC 60.826 66.667 0.00 0.00 0.00 4.61
74 75 4.115199 ATTCTCCTGCCGCCCACC 62.115 66.667 0.00 0.00 0.00 4.61
79 80 4.864334 CCTGCCGCCCACCTCATC 62.864 72.222 0.00 0.00 0.00 2.92
80 81 4.864334 CTGCCGCCCACCTCATCC 62.864 72.222 0.00 0.00 0.00 3.51
82 83 4.864334 GCCGCCCACCTCATCCTG 62.864 72.222 0.00 0.00 0.00 3.86
83 84 4.864334 CCGCCCACCTCATCCTGC 62.864 72.222 0.00 0.00 0.00 4.85
84 85 3.790437 CGCCCACCTCATCCTGCT 61.790 66.667 0.00 0.00 0.00 4.24
85 86 2.434843 CGCCCACCTCATCCTGCTA 61.435 63.158 0.00 0.00 0.00 3.49
86 87 1.449353 GCCCACCTCATCCTGCTAG 59.551 63.158 0.00 0.00 0.00 3.42
87 88 1.341156 GCCCACCTCATCCTGCTAGT 61.341 60.000 0.00 0.00 0.00 2.57
88 89 1.207791 CCCACCTCATCCTGCTAGTT 58.792 55.000 0.00 0.00 0.00 2.24
89 90 1.134280 CCCACCTCATCCTGCTAGTTG 60.134 57.143 0.00 0.00 0.00 3.16
90 91 1.134280 CCACCTCATCCTGCTAGTTGG 60.134 57.143 0.00 0.00 0.00 3.77
91 92 1.134280 CACCTCATCCTGCTAGTTGGG 60.134 57.143 0.00 0.00 0.00 4.12
92 93 1.207791 CCTCATCCTGCTAGTTGGGT 58.792 55.000 0.00 0.00 0.00 4.51
93 94 1.134280 CCTCATCCTGCTAGTTGGGTG 60.134 57.143 9.29 9.29 35.86 4.61
94 95 1.833630 CTCATCCTGCTAGTTGGGTGA 59.166 52.381 15.15 15.15 40.77 4.02
95 96 2.237143 CTCATCCTGCTAGTTGGGTGAA 59.763 50.000 16.22 5.19 42.22 3.18
96 97 2.237143 TCATCCTGCTAGTTGGGTGAAG 59.763 50.000 14.08 0.00 40.17 3.02
97 98 0.324943 TCCTGCTAGTTGGGTGAAGC 59.675 55.000 0.00 0.00 35.51 3.86
98 99 0.326264 CCTGCTAGTTGGGTGAAGCT 59.674 55.000 0.00 0.00 35.95 3.74
99 100 1.555075 CCTGCTAGTTGGGTGAAGCTA 59.445 52.381 0.00 0.00 35.95 3.32
100 101 2.027192 CCTGCTAGTTGGGTGAAGCTAA 60.027 50.000 0.00 0.00 35.95 3.09
101 102 3.559171 CCTGCTAGTTGGGTGAAGCTAAA 60.559 47.826 0.00 0.00 35.95 1.85
102 103 4.072131 CTGCTAGTTGGGTGAAGCTAAAA 58.928 43.478 0.00 0.00 35.95 1.52
103 104 4.465886 TGCTAGTTGGGTGAAGCTAAAAA 58.534 39.130 0.00 0.00 35.95 1.94
138 139 5.353938 CGAAAGGGGAACTATATCGAAACA 58.646 41.667 0.00 0.00 34.03 2.83
142 143 4.658901 AGGGGAACTATATCGAAACACCAT 59.341 41.667 0.00 0.00 0.00 3.55
149 150 6.150318 ACTATATCGAAACACCATCATCGTC 58.850 40.000 0.00 0.00 36.70 4.20
157 158 1.068083 CCATCATCGTCCCGACCTG 59.932 63.158 0.00 0.00 39.18 4.00
398 405 7.043961 TGATACTTGATACAGGACATGACTC 57.956 40.000 0.00 0.00 0.00 3.36
445 456 5.241728 TGGAGAGATCATATACGTGTTCCTG 59.758 44.000 0.00 0.00 0.00 3.86
480 491 6.648725 ACTTTGCTCGTCATATCTAACAAC 57.351 37.500 0.00 0.00 0.00 3.32
483 494 7.334421 ACTTTGCTCGTCATATCTAACAACAAT 59.666 33.333 0.00 0.00 0.00 2.71
519 536 2.933906 CAAACTGATAACGTGCCGGTAT 59.066 45.455 1.90 5.04 42.74 2.73
546 570 7.797123 CGAACACTGATCAATGATACATTGATG 59.203 37.037 31.07 23.66 45.59 3.07
549 573 7.067737 ACACTGATCAATGATACATTGATGCAA 59.932 33.333 31.07 20.07 45.59 4.08
564 588 3.984292 GCAAGTACATGCAGTGAGC 57.016 52.632 17.73 0.00 45.70 4.26
567 591 1.736126 CAAGTACATGCAGTGAGCCAG 59.264 52.381 0.00 0.00 44.83 4.85
568 592 0.979665 AGTACATGCAGTGAGCCAGT 59.020 50.000 0.00 0.00 44.83 4.00
569 593 1.081892 GTACATGCAGTGAGCCAGTG 58.918 55.000 0.00 5.84 44.83 3.66
570 594 0.975887 TACATGCAGTGAGCCAGTGA 59.024 50.000 12.53 1.31 44.83 3.41
571 595 0.321387 ACATGCAGTGAGCCAGTGAG 60.321 55.000 12.53 5.55 44.83 3.51
572 596 0.321387 CATGCAGTGAGCCAGTGAGT 60.321 55.000 12.53 0.05 44.83 3.41
573 597 0.036577 ATGCAGTGAGCCAGTGAGTC 60.037 55.000 12.53 0.00 44.83 3.36
574 598 1.368950 GCAGTGAGCCAGTGAGTCA 59.631 57.895 12.53 0.00 36.99 3.41
575 599 0.036577 GCAGTGAGCCAGTGAGTCAT 60.037 55.000 12.53 0.00 36.99 3.06
591 615 0.735978 TCATCTACGCACGGCTGTTG 60.736 55.000 0.00 0.00 0.00 3.33
608 632 4.558697 GCTGTTGAACTGGGACCAAAATAC 60.559 45.833 4.40 0.00 0.00 1.89
648 683 0.537143 AACAAATGAGTGCAGCCCGA 60.537 50.000 0.00 0.00 0.00 5.14
652 687 0.745845 AATGAGTGCAGCCCGATCAC 60.746 55.000 0.00 0.00 0.00 3.06
653 688 2.887568 GAGTGCAGCCCGATCACG 60.888 66.667 0.00 0.00 35.97 4.35
742 781 6.597280 AGAAGCAAAATAACTGGCAAACAAAA 59.403 30.769 0.00 0.00 0.00 2.44
807 846 2.540265 ATTGATCGATCCAGCTCACC 57.460 50.000 22.31 0.00 0.00 4.02
908 953 2.136878 CATCCTCCTCCCAGTCCCG 61.137 68.421 0.00 0.00 0.00 5.14
922 969 1.917568 AGTCCCGGTGGCCTATAAAAA 59.082 47.619 3.32 0.00 0.00 1.94
1050 1104 1.294459 CTCTGTGCTGCCACTGCTA 59.706 57.895 0.00 0.00 42.54 3.49
1167 1221 2.575993 CTCCTGACGCTGTCCCTG 59.424 66.667 6.30 0.00 0.00 4.45
1584 1695 1.860950 CATCCTGTACGTAGCATGCAC 59.139 52.381 21.98 14.60 0.00 4.57
1624 1747 1.554160 TCTACCTCTTCTCCTCGACGT 59.446 52.381 0.00 0.00 0.00 4.34
1627 1750 1.554160 ACCTCTTCTCCTCGACGTAGA 59.446 52.381 0.00 0.00 0.00 2.59
1628 1751 2.206750 CCTCTTCTCCTCGACGTAGAG 58.793 57.143 17.74 17.74 37.97 2.43
1650 1776 0.179702 AGATCTCATGCATGCACCGT 59.820 50.000 25.37 4.03 0.00 4.83
1651 1777 1.019673 GATCTCATGCATGCACCGTT 58.980 50.000 25.37 3.57 0.00 4.44
1652 1778 1.003116 GATCTCATGCATGCACCGTTC 60.003 52.381 25.37 14.04 0.00 3.95
1653 1779 1.026182 TCTCATGCATGCACCGTTCC 61.026 55.000 25.37 0.00 0.00 3.62
1654 1780 1.002257 TCATGCATGCACCGTTCCT 60.002 52.632 25.37 1.29 0.00 3.36
1655 1781 1.026182 TCATGCATGCACCGTTCCTC 61.026 55.000 25.37 0.00 0.00 3.71
1656 1782 1.750399 ATGCATGCACCGTTCCTCC 60.750 57.895 25.37 0.00 0.00 4.30
1657 1783 3.134127 GCATGCACCGTTCCTCCC 61.134 66.667 14.21 0.00 0.00 4.30
2048 2174 0.108138 GAGTGCGCCACCAAGTAGAT 60.108 55.000 4.18 0.00 34.49 1.98
2049 2175 0.108138 AGTGCGCCACCAAGTAGATC 60.108 55.000 4.18 0.00 34.49 2.75
2050 2176 1.153647 TGCGCCACCAAGTAGATCG 60.154 57.895 4.18 0.00 0.00 3.69
2051 2177 1.141019 GCGCCACCAAGTAGATCGA 59.859 57.895 0.00 0.00 0.00 3.59
2065 2191 2.520069 AGATCGAGTGTTCTGTCTGGT 58.480 47.619 0.00 0.00 0.00 4.00
2076 2202 3.712881 GTCTGGTGGCGACGTTGC 61.713 66.667 19.96 19.96 0.00 4.17
2152 2282 6.007936 TGGATGTAAATGTAACTGTGCAAC 57.992 37.500 0.00 0.00 37.35 4.17
2188 2318 9.245962 GATACAATAAATTCAGCGTACACTACT 57.754 33.333 0.00 0.00 0.00 2.57
2201 2331 6.918569 AGCGTACACTACTTAATTAGAGCATG 59.081 38.462 6.84 0.00 0.00 4.06
2271 2405 3.430790 CCTGACCGAGCACTCATCAAATA 60.431 47.826 0.00 0.00 0.00 1.40
2416 2568 3.094062 GCCTGACTCCGGCAGCATA 62.094 63.158 6.61 0.00 46.77 3.14
2527 2733 1.965219 CTCCCGTCGAAGGAACTGT 59.035 57.895 19.75 0.00 40.86 3.55
2536 2742 0.250338 GAAGGAACTGTCGGTTGGCT 60.250 55.000 0.56 0.00 40.86 4.75
2555 2761 2.487805 GCTTCCACATATGCCTCATCCA 60.488 50.000 1.58 0.00 0.00 3.41
2704 2954 1.047002 CCTCCATCAGCTCTGGTAGG 58.953 60.000 10.85 11.64 35.19 3.18
2725 2975 0.032615 GCTCTCCCTTCTCCTCCTCA 60.033 60.000 0.00 0.00 0.00 3.86
2726 2976 1.621072 GCTCTCCCTTCTCCTCCTCAA 60.621 57.143 0.00 0.00 0.00 3.02
2873 3214 1.586564 GTCGGGATCTTGCGTCGAG 60.587 63.158 0.00 0.00 0.00 4.04
2906 3279 4.742649 AGAGCGTGGGAGAGCGGA 62.743 66.667 0.00 0.00 38.61 5.54
2965 3339 1.213296 GGAAGAGGTGGATGGGCTAA 58.787 55.000 0.00 0.00 0.00 3.09
3003 3377 5.061179 GGCCGACTTAAATAGCTGGATTTA 58.939 41.667 0.00 0.00 31.51 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.147587 GGTGATGGCATGGGGGCT 62.148 66.667 3.81 0.00 43.83 5.19
5 6 4.854924 TCGGCGGTGATGGCATGG 62.855 66.667 3.81 0.00 0.00 3.66
6 7 3.576356 GTCGGCGGTGATGGCATG 61.576 66.667 3.81 0.00 0.00 4.06
7 8 3.329542 AAGTCGGCGGTGATGGCAT 62.330 57.895 7.21 0.00 0.00 4.40
8 9 3.950794 GAAGTCGGCGGTGATGGCA 62.951 63.158 7.21 0.00 0.00 4.92
9 10 3.195698 GAAGTCGGCGGTGATGGC 61.196 66.667 7.21 0.00 0.00 4.40
10 11 2.511600 GGAAGTCGGCGGTGATGG 60.512 66.667 7.21 0.00 0.00 3.51
11 12 2.100631 GTGGAAGTCGGCGGTGATG 61.101 63.158 7.21 0.00 0.00 3.07
12 13 2.264794 GTGGAAGTCGGCGGTGAT 59.735 61.111 7.21 0.00 0.00 3.06
13 14 3.998672 GGTGGAAGTCGGCGGTGA 61.999 66.667 7.21 0.00 0.00 4.02
19 20 4.096003 ATGCCCGGTGGAAGTCGG 62.096 66.667 0.00 0.00 45.29 4.79
20 21 2.511600 GATGCCCGGTGGAAGTCG 60.512 66.667 0.00 0.00 0.00 4.18
21 22 1.745489 GTGATGCCCGGTGGAAGTC 60.745 63.158 0.00 0.00 0.00 3.01
22 23 2.224159 AGTGATGCCCGGTGGAAGT 61.224 57.895 0.00 0.00 0.00 3.01
23 24 1.746615 CAGTGATGCCCGGTGGAAG 60.747 63.158 0.00 0.00 0.00 3.46
24 25 2.350895 CAGTGATGCCCGGTGGAA 59.649 61.111 0.00 0.00 0.00 3.53
25 26 4.408821 GCAGTGATGCCCGGTGGA 62.409 66.667 0.00 0.00 0.00 4.02
33 34 3.364441 TTGTGGCGGCAGTGATGC 61.364 61.111 13.91 0.00 0.00 3.91
34 35 2.562912 GTTGTGGCGGCAGTGATG 59.437 61.111 13.91 0.00 0.00 3.07
35 36 3.049674 CGTTGTGGCGGCAGTGAT 61.050 61.111 13.91 0.00 0.00 3.06
42 43 3.609214 GAATGGTGCGTTGTGGCGG 62.609 63.158 0.00 0.00 35.06 6.13
43 44 2.126888 GAATGGTGCGTTGTGGCG 60.127 61.111 0.00 0.00 35.06 5.69
44 45 1.210155 GAGAATGGTGCGTTGTGGC 59.790 57.895 0.00 0.00 0.00 5.01
45 46 0.606401 AGGAGAATGGTGCGTTGTGG 60.606 55.000 0.00 0.00 0.00 4.17
46 47 0.518636 CAGGAGAATGGTGCGTTGTG 59.481 55.000 0.00 0.00 0.00 3.33
47 48 1.237285 GCAGGAGAATGGTGCGTTGT 61.237 55.000 0.00 0.00 0.00 3.32
48 49 1.503542 GCAGGAGAATGGTGCGTTG 59.496 57.895 0.00 0.00 0.00 4.10
49 50 1.675641 GGCAGGAGAATGGTGCGTT 60.676 57.895 0.00 0.00 38.13 4.84
50 51 2.045926 GGCAGGAGAATGGTGCGT 60.046 61.111 0.00 0.00 38.13 5.24
51 52 3.197790 CGGCAGGAGAATGGTGCG 61.198 66.667 0.00 0.00 38.13 5.34
52 53 3.512516 GCGGCAGGAGAATGGTGC 61.513 66.667 0.00 0.00 36.42 5.01
53 54 2.825836 GGCGGCAGGAGAATGGTG 60.826 66.667 3.07 0.00 0.00 4.17
54 55 4.115199 GGGCGGCAGGAGAATGGT 62.115 66.667 12.47 0.00 0.00 3.55
55 56 4.113815 TGGGCGGCAGGAGAATGG 62.114 66.667 12.47 0.00 0.00 3.16
56 57 2.825836 GTGGGCGGCAGGAGAATG 60.826 66.667 12.47 0.00 0.00 2.67
57 58 4.115199 GGTGGGCGGCAGGAGAAT 62.115 66.667 12.47 0.00 0.00 2.40
62 63 4.864334 GATGAGGTGGGCGGCAGG 62.864 72.222 12.47 0.00 0.00 4.85
63 64 4.864334 GGATGAGGTGGGCGGCAG 62.864 72.222 12.47 0.00 0.00 4.85
65 66 4.864334 CAGGATGAGGTGGGCGGC 62.864 72.222 0.00 0.00 39.69 6.53
66 67 4.864334 GCAGGATGAGGTGGGCGG 62.864 72.222 0.00 0.00 39.69 6.13
67 68 2.374830 CTAGCAGGATGAGGTGGGCG 62.375 65.000 0.00 0.00 39.69 6.13
68 69 1.341156 ACTAGCAGGATGAGGTGGGC 61.341 60.000 0.00 0.00 39.69 5.36
69 70 1.134280 CAACTAGCAGGATGAGGTGGG 60.134 57.143 0.00 0.00 39.69 4.61
70 71 1.134280 CCAACTAGCAGGATGAGGTGG 60.134 57.143 0.00 0.00 40.79 4.61
71 72 1.134280 CCCAACTAGCAGGATGAGGTG 60.134 57.143 2.72 0.00 39.69 4.00
72 73 1.207791 CCCAACTAGCAGGATGAGGT 58.792 55.000 2.72 0.00 39.69 3.85
73 74 1.134280 CACCCAACTAGCAGGATGAGG 60.134 57.143 2.72 0.00 39.69 3.86
74 75 1.833630 TCACCCAACTAGCAGGATGAG 59.166 52.381 2.72 0.00 39.69 2.90
75 76 1.951209 TCACCCAACTAGCAGGATGA 58.049 50.000 2.72 0.00 39.69 2.92
76 77 2.636830 CTTCACCCAACTAGCAGGATG 58.363 52.381 2.72 0.00 40.87 3.51
77 78 1.065126 GCTTCACCCAACTAGCAGGAT 60.065 52.381 2.72 0.00 33.88 3.24
78 79 0.324943 GCTTCACCCAACTAGCAGGA 59.675 55.000 2.72 0.00 33.88 3.86
79 80 0.326264 AGCTTCACCCAACTAGCAGG 59.674 55.000 0.00 0.00 36.11 4.85
80 81 3.334583 TTAGCTTCACCCAACTAGCAG 57.665 47.619 0.00 0.00 36.11 4.24
81 82 3.780804 TTTAGCTTCACCCAACTAGCA 57.219 42.857 0.00 0.00 36.11 3.49
101 102 1.554617 CCTTTCGGGGGCATCATTTTT 59.445 47.619 0.00 0.00 0.00 1.94
102 103 1.194218 CCTTTCGGGGGCATCATTTT 58.806 50.000 0.00 0.00 0.00 1.82
103 104 2.900547 CCTTTCGGGGGCATCATTT 58.099 52.632 0.00 0.00 0.00 2.32
104 105 4.684623 CCTTTCGGGGGCATCATT 57.315 55.556 0.00 0.00 0.00 2.57
114 115 4.595762 TTCGATATAGTTCCCCTTTCGG 57.404 45.455 0.00 0.00 0.00 4.30
127 128 5.466819 GGACGATGATGGTGTTTCGATATA 58.533 41.667 0.00 0.00 35.64 0.86
157 158 0.178301 GAGAAACCCCAGACCCGATC 59.822 60.000 0.00 0.00 0.00 3.69
202 204 4.742201 GCGTCGAAGGGCTGCTCA 62.742 66.667 0.74 0.00 0.00 4.26
376 381 5.508153 GCGAGTCATGTCCTGTATCAAGTAT 60.508 44.000 0.00 0.00 0.00 2.12
398 405 0.306533 AGTACGCCAAGTTGTTTGCG 59.693 50.000 19.21 19.21 40.05 4.85
445 456 3.877508 ACGAGCAAAGTTATGATTAGGCC 59.122 43.478 0.00 0.00 0.00 5.19
480 491 3.861276 TTGGAGCAAGATTCTGCATTG 57.139 42.857 9.67 0.00 45.18 2.82
483 494 2.555325 CAGTTTGGAGCAAGATTCTGCA 59.445 45.455 9.67 0.00 45.18 4.41
519 536 7.041107 TCAATGTATCATTGATCAGTGTTCGA 58.959 34.615 16.80 0.00 33.55 3.71
520 537 7.237920 TCAATGTATCATTGATCAGTGTTCG 57.762 36.000 16.80 2.32 33.55 3.95
546 570 0.449388 GGCTCACTGCATGTACTTGC 59.551 55.000 23.09 23.09 45.15 4.01
549 573 0.979665 ACTGGCTCACTGCATGTACT 59.020 50.000 0.00 0.00 45.15 2.73
564 588 1.795525 CGTGCGTAGATGACTCACTGG 60.796 57.143 0.00 0.00 40.89 4.00
567 591 1.140407 GCCGTGCGTAGATGACTCAC 61.140 60.000 0.00 0.00 39.87 3.51
568 592 1.138883 GCCGTGCGTAGATGACTCA 59.861 57.895 0.00 0.00 0.00 3.41
569 593 0.867753 CAGCCGTGCGTAGATGACTC 60.868 60.000 0.00 0.00 0.00 3.36
570 594 1.139734 CAGCCGTGCGTAGATGACT 59.860 57.895 0.00 0.00 0.00 3.41
571 595 0.736325 AACAGCCGTGCGTAGATGAC 60.736 55.000 0.00 0.00 0.00 3.06
572 596 0.735978 CAACAGCCGTGCGTAGATGA 60.736 55.000 0.00 0.00 0.00 2.92
573 597 0.735978 TCAACAGCCGTGCGTAGATG 60.736 55.000 0.00 0.00 0.00 2.90
574 598 0.037697 TTCAACAGCCGTGCGTAGAT 60.038 50.000 0.00 0.00 0.00 1.98
575 599 0.942410 GTTCAACAGCCGTGCGTAGA 60.942 55.000 0.00 0.00 0.00 2.59
591 615 3.404899 TCACGTATTTTGGTCCCAGTTC 58.595 45.455 0.00 0.00 0.00 3.01
608 632 2.258591 CAGGTCCGGTGACTCACG 59.741 66.667 0.00 0.00 41.47 4.35
619 643 0.804989 CTCATTTGTTCGGCAGGTCC 59.195 55.000 0.00 0.00 0.00 4.46
635 670 2.265739 GTGATCGGGCTGCACTCA 59.734 61.111 0.00 0.00 0.00 3.41
653 688 4.794439 GGAAACATTGGCGCCCGC 62.794 66.667 26.77 3.71 41.06 6.13
663 701 1.176527 CTTGGATGGCGTGGAAACAT 58.823 50.000 0.00 0.00 46.14 2.71
807 846 5.337169 CCAGAGAAAGAGAGGAAGGTTGTAG 60.337 48.000 0.00 0.00 0.00 2.74
922 969 2.518349 CCGGGTGCAAGTTGTGGT 60.518 61.111 4.48 0.00 0.00 4.16
1584 1695 1.255882 AGAGAGAGACTGGTGCTGTG 58.744 55.000 0.00 0.00 0.00 3.66
1591 1702 4.503714 AGAGGTAGAAGAGAGAGACTGG 57.496 50.000 0.00 0.00 0.00 4.00
1624 1747 3.181458 TGCATGCATGAGATCTTGCTCTA 60.181 43.478 30.64 1.49 44.41 2.43
1627 1750 1.676529 GTGCATGCATGAGATCTTGCT 59.323 47.619 30.64 3.94 44.41 3.91
1628 1751 1.269102 GGTGCATGCATGAGATCTTGC 60.269 52.381 30.64 14.24 44.38 4.01
1653 1779 0.179073 CGTAGAACCTGCATGGGGAG 60.179 60.000 0.00 0.00 41.11 4.30
1654 1780 0.907704 ACGTAGAACCTGCATGGGGA 60.908 55.000 0.00 0.00 41.11 4.81
1655 1781 0.744414 CACGTAGAACCTGCATGGGG 60.744 60.000 7.06 0.00 41.11 4.96
1656 1782 0.744414 CCACGTAGAACCTGCATGGG 60.744 60.000 7.06 0.00 41.11 4.00
1657 1783 0.249120 TCCACGTAGAACCTGCATGG 59.751 55.000 0.00 0.00 42.93 3.66
2048 2174 0.673985 CCACCAGACAGAACACTCGA 59.326 55.000 0.00 0.00 0.00 4.04
2049 2175 0.946221 GCCACCAGACAGAACACTCG 60.946 60.000 0.00 0.00 0.00 4.18
2050 2176 0.946221 CGCCACCAGACAGAACACTC 60.946 60.000 0.00 0.00 0.00 3.51
2051 2177 1.069765 CGCCACCAGACAGAACACT 59.930 57.895 0.00 0.00 0.00 3.55
2077 2203 5.458041 TCTATAAAAATACTCCGACCCCG 57.542 43.478 0.00 0.00 0.00 5.73
2113 2240 3.130516 ACATCCATACGTAGGTGTGACAG 59.869 47.826 13.16 5.42 37.45 3.51
2182 2312 8.818057 GGTTGTACATGCTCTAATTAAGTAGTG 58.182 37.037 9.60 8.47 0.00 2.74
2188 2318 5.179533 TGCGGTTGTACATGCTCTAATTAA 58.820 37.500 14.04 0.00 0.00 1.40
2201 2331 8.013378 GGTTATATTTGTCATATGCGGTTGTAC 58.987 37.037 0.00 0.00 0.00 2.90
2257 2391 7.094248 TGCAGTTGTATTTATTTGATGAGTGCT 60.094 33.333 0.00 0.00 33.39 4.40
2271 2405 3.066291 TGTCCGGATGCAGTTGTATTT 57.934 42.857 7.81 0.00 0.00 1.40
2503 2709 4.069232 CTTCGACGGGAGCAGGCA 62.069 66.667 0.00 0.00 0.00 4.75
2527 2733 2.016604 GCATATGTGGAAGCCAACCGA 61.017 52.381 4.29 0.00 34.18 4.69
2536 2742 2.107031 CCTGGATGAGGCATATGTGGAA 59.893 50.000 4.29 0.00 34.01 3.53
2561 2767 1.065126 GTAGCAGGCCATTCTGGAGTT 60.065 52.381 5.01 0.00 40.96 3.01
2704 2954 0.325203 AGGAGGAGAAGGGAGAGCAC 60.325 60.000 0.00 0.00 0.00 4.40
2906 3279 2.048503 CCGTCCGCCTCGTTTCTT 60.049 61.111 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.