Multiple sequence alignment - TraesCS3D01G127600

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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 TraesCS3D01G127600 chr3D 100.000 5172 0 0 1 5172 85412834 85407663 0.000000e+00 9551
1 TraesCS3D01G127600 chr3D 79.303 918 117 42 1776 2647 84900697 84899807 4.490000e-160 575
2 TraesCS3D01G127600 chr3D 77.233 918 179 23 1761 2671 85443100 85443994 1.280000e-140 510
3 TraesCS3D01G127600 chr3D 78.023 860 150 24 1819 2666 85399498 85400330 5.980000e-139 505
4 TraesCS3D01G127600 chr3D 81.058 586 90 19 3940 4516 85247262 85247835 1.020000e-121 448
5 TraesCS3D01G127600 chr3D 78.902 583 92 19 3940 4515 84898935 84898377 2.940000e-97 366
6 TraesCS3D01G127600 chr3D 86.822 258 27 4 4896 5150 422528803 422529056 1.100000e-71 281
7 TraesCS3D01G127600 chr3D 77.011 348 63 10 3362 3697 84034760 84034418 3.180000e-42 183
8 TraesCS3D01G127600 chrUn 96.707 1245 33 5 1428 2671 297430764 297432001 0.000000e+00 2065
9 TraesCS3D01G127600 chrUn 96.707 1245 33 5 1428 2671 297435716 297436953 0.000000e+00 2065
10 TraesCS3D01G127600 chrUn 94.329 864 16 7 3326 4183 464235687 464234851 0.000000e+00 1293
11 TraesCS3D01G127600 chrUn 90.658 653 61 0 3 655 33838906 33839558 0.000000e+00 869
12 TraesCS3D01G127600 chrUn 86.364 528 69 2 2672 3199 82338025 82337501 1.620000e-159 573
13 TraesCS3D01G127600 chrUn 91.667 336 17 4 885 1216 297430022 297430350 6.110000e-124 455
14 TraesCS3D01G127600 chrUn 91.667 336 17 4 885 1216 297434974 297435302 6.110000e-124 455
15 TraesCS3D01G127600 chrUn 93.269 208 6 2 1224 1430 297430461 297430661 3.030000e-77 300
16 TraesCS3D01G127600 chrUn 93.269 208 6 2 1224 1430 297435413 297435613 3.030000e-77 300
17 TraesCS3D01G127600 chrUn 95.652 115 3 1 662 774 297429900 297430014 3.180000e-42 183
18 TraesCS3D01G127600 chrUn 95.652 115 3 1 662 774 297434852 297434966 3.180000e-42 183
19 TraesCS3D01G127600 chr3A 96.056 1065 29 6 3362 4417 102299707 102298647 0.000000e+00 1722
20 TraesCS3D01G127600 chr3A 95.201 896 35 4 1487 2380 102308221 102307332 0.000000e+00 1410
21 TraesCS3D01G127600 chr3A 95.125 759 33 1 4414 5172 102293427 102292673 0.000000e+00 1194
22 TraesCS3D01G127600 chr3A 78.936 902 133 33 1776 2636 101870654 101869769 1.260000e-155 560
23 TraesCS3D01G127600 chr3A 97.232 289 7 1 2377 2665 102300369 102300082 6.020000e-134 488
24 TraesCS3D01G127600 chr3A 77.608 786 154 19 1761 2544 102523819 102524584 1.700000e-124 457
25 TraesCS3D01G127600 chr3A 77.538 788 151 22 1761 2544 102472982 102473747 7.900000e-123 451
26 TraesCS3D01G127600 chr3A 76.265 771 141 28 1914 2671 102359665 102360406 6.320000e-99 372
27 TraesCS3D01G127600 chr3A 99.034 207 1 1 3200 3405 102299914 102299708 2.270000e-98 370
28 TraesCS3D01G127600 chr3A 88.259 247 22 4 4896 5139 566874625 566874383 6.550000e-74 289
29 TraesCS3D01G127600 chr3A 79.762 336 56 11 3940 4272 101868895 101868569 3.110000e-57 233
30 TraesCS3D01G127600 chr3A 96.721 122 4 0 674 795 102309644 102309523 2.440000e-48 204
31 TraesCS3D01G127600 chr3A 94.792 96 4 1 1401 1495 102309061 102308966 1.160000e-31 148
32 TraesCS3D01G127600 chr3A 95.745 47 1 1 1325 1371 102309096 102309051 2.000000e-09 75
33 TraesCS3D01G127600 chr3B 95.657 990 39 4 4185 5172 134984796 134983809 0.000000e+00 1587
34 TraesCS3D01G127600 chr3B 95.657 990 39 4 4185 5172 134984897 134985884 0.000000e+00 1587
35 TraesCS3D01G127600 chr3B 87.443 661 78 3 1 660 119059582 119060238 0.000000e+00 756
36 TraesCS3D01G127600 chr3B 82.276 536 70 17 1820 2343 133806561 133806039 1.710000e-119 440
37 TraesCS3D01G127600 chr3B 80.218 551 79 20 3972 4515 133804819 133804292 2.260000e-103 387
38 TraesCS3D01G127600 chr3B 76.485 421 77 17 2255 2671 135680323 135680725 5.250000e-50 209
39 TraesCS3D01G127600 chr4A 90.505 653 62 0 3 655 659486193 659485541 0.000000e+00 863
40 TraesCS3D01G127600 chr4A 90.505 653 62 0 3 655 659548212 659547560 0.000000e+00 863
41 TraesCS3D01G127600 chr4A 90.046 653 62 1 3 655 659456093 659455444 0.000000e+00 843
42 TraesCS3D01G127600 chr5A 90.181 662 63 1 1 660 24430784 24431445 0.000000e+00 861
43 TraesCS3D01G127600 chr5A 86.932 528 66 2 2672 3199 311003988 311004512 1.600000e-164 590
44 TraesCS3D01G127600 chr2D 86.057 667 80 7 1 660 148815405 148816065 0.000000e+00 704
45 TraesCS3D01G127600 chr2D 88.158 532 60 2 2668 3199 204489170 204488642 9.450000e-177 630
46 TraesCS3D01G127600 chr5B 85.090 664 88 7 1 660 493965070 493965726 0.000000e+00 667
47 TraesCS3D01G127600 chr5B 87.308 260 21 6 4896 5151 327083783 327083532 2.360000e-73 287
48 TraesCS3D01G127600 chr6B 84.465 663 99 2 1 663 680949489 680948831 0.000000e+00 651
49 TraesCS3D01G127600 chr5D 87.879 528 61 2 2672 3199 545219692 545219168 7.360000e-173 617
50 TraesCS3D01G127600 chr5D 87.805 246 24 4 4896 5138 517846694 517846936 3.050000e-72 283
51 TraesCS3D01G127600 chr2A 87.140 521 60 3 2676 3196 151262723 151263236 7.460000e-163 584
52 TraesCS3D01G127600 chr2A 86.364 528 69 2 2672 3199 610714595 610715119 1.620000e-159 573
53 TraesCS3D01G127600 chr2A 88.760 258 21 5 4896 5150 177658421 177658673 5.030000e-80 309
54 TraesCS3D01G127600 chr7A 86.616 523 67 2 2671 3193 551094284 551093765 4.490000e-160 575
55 TraesCS3D01G127600 chr1A 86.364 528 69 2 2672 3199 516145187 516145711 1.620000e-159 573
56 TraesCS3D01G127600 chr6A 86.064 531 71 2 2669 3199 222690405 222690932 7.520000e-158 568
57 TraesCS3D01G127600 chr2B 88.760 258 19 7 4896 5150 225571381 225571631 1.810000e-79 307


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 TraesCS3D01G127600 chr3D 85407663 85412834 5171 True 9551.00 9551 100.000000 1 5172 1 chr3D.!!$R2 5171
1 TraesCS3D01G127600 chr3D 85443100 85443994 894 False 510.00 510 77.233000 1761 2671 1 chr3D.!!$F3 910
2 TraesCS3D01G127600 chr3D 85399498 85400330 832 False 505.00 505 78.023000 1819 2666 1 chr3D.!!$F2 847
3 TraesCS3D01G127600 chr3D 84898377 84900697 2320 True 470.50 575 79.102500 1776 4515 2 chr3D.!!$R3 2739
4 TraesCS3D01G127600 chr3D 85247262 85247835 573 False 448.00 448 81.058000 3940 4516 1 chr3D.!!$F1 576
5 TraesCS3D01G127600 chrUn 464234851 464235687 836 True 1293.00 1293 94.329000 3326 4183 1 chrUn.!!$R2 857
6 TraesCS3D01G127600 chrUn 33838906 33839558 652 False 869.00 869 90.658000 3 655 1 chrUn.!!$F1 652
7 TraesCS3D01G127600 chrUn 297429900 297436953 7053 False 750.75 2065 94.323750 662 2671 8 chrUn.!!$F2 2009
8 TraesCS3D01G127600 chrUn 82337501 82338025 524 True 573.00 573 86.364000 2672 3199 1 chrUn.!!$R1 527
9 TraesCS3D01G127600 chr3A 102292673 102293427 754 True 1194.00 1194 95.125000 4414 5172 1 chr3A.!!$R1 758
10 TraesCS3D01G127600 chr3A 102298647 102300369 1722 True 860.00 1722 97.440667 2377 4417 3 chr3A.!!$R4 2040
11 TraesCS3D01G127600 chr3A 102307332 102309644 2312 True 459.25 1410 95.614750 674 2380 4 chr3A.!!$R5 1706
12 TraesCS3D01G127600 chr3A 102523819 102524584 765 False 457.00 457 77.608000 1761 2544 1 chr3A.!!$F3 783
13 TraesCS3D01G127600 chr3A 102472982 102473747 765 False 451.00 451 77.538000 1761 2544 1 chr3A.!!$F2 783
14 TraesCS3D01G127600 chr3A 101868569 101870654 2085 True 396.50 560 79.349000 1776 4272 2 chr3A.!!$R3 2496
15 TraesCS3D01G127600 chr3A 102359665 102360406 741 False 372.00 372 76.265000 1914 2671 1 chr3A.!!$F1 757
16 TraesCS3D01G127600 chr3B 134983809 134984796 987 True 1587.00 1587 95.657000 4185 5172 1 chr3B.!!$R1 987
17 TraesCS3D01G127600 chr3B 134984897 134985884 987 False 1587.00 1587 95.657000 4185 5172 1 chr3B.!!$F2 987
18 TraesCS3D01G127600 chr3B 119059582 119060238 656 False 756.00 756 87.443000 1 660 1 chr3B.!!$F1 659
19 TraesCS3D01G127600 chr3B 133804292 133806561 2269 True 413.50 440 81.247000 1820 4515 2 chr3B.!!$R2 2695
20 TraesCS3D01G127600 chr4A 659485541 659486193 652 True 863.00 863 90.505000 3 655 1 chr4A.!!$R2 652
21 TraesCS3D01G127600 chr4A 659547560 659548212 652 True 863.00 863 90.505000 3 655 1 chr4A.!!$R3 652
22 TraesCS3D01G127600 chr4A 659455444 659456093 649 True 843.00 843 90.046000 3 655 1 chr4A.!!$R1 652
23 TraesCS3D01G127600 chr5A 24430784 24431445 661 False 861.00 861 90.181000 1 660 1 chr5A.!!$F1 659
24 TraesCS3D01G127600 chr5A 311003988 311004512 524 False 590.00 590 86.932000 2672 3199 1 chr5A.!!$F2 527
25 TraesCS3D01G127600 chr2D 148815405 148816065 660 False 704.00 704 86.057000 1 660 1 chr2D.!!$F1 659
26 TraesCS3D01G127600 chr2D 204488642 204489170 528 True 630.00 630 88.158000 2668 3199 1 chr2D.!!$R1 531
27 TraesCS3D01G127600 chr5B 493965070 493965726 656 False 667.00 667 85.090000 1 660 1 chr5B.!!$F1 659
28 TraesCS3D01G127600 chr6B 680948831 680949489 658 True 651.00 651 84.465000 1 663 1 chr6B.!!$R1 662
29 TraesCS3D01G127600 chr5D 545219168 545219692 524 True 617.00 617 87.879000 2672 3199 1 chr5D.!!$R1 527
30 TraesCS3D01G127600 chr2A 151262723 151263236 513 False 584.00 584 87.140000 2676 3196 1 chr2A.!!$F1 520
31 TraesCS3D01G127600 chr2A 610714595 610715119 524 False 573.00 573 86.364000 2672 3199 1 chr2A.!!$F3 527
32 TraesCS3D01G127600 chr7A 551093765 551094284 519 True 575.00 575 86.616000 2671 3193 1 chr7A.!!$R1 522
33 TraesCS3D01G127600 chr1A 516145187 516145711 524 False 573.00 573 86.364000 2672 3199 1 chr1A.!!$F1 527
34 TraesCS3D01G127600 chr6A 222690405 222690932 527 False 568.00 568 86.064000 2669 3199 1 chr6A.!!$F1 530

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
854 869 0.609131 AGCACCAATACGCAAAGGCT 60.609 50.000 0.00 0.00 38.10 4.58 F
1316 1445 0.392706 ACTGAATCTGCCACGTCACA 59.607 50.000 0.00 0.00 0.00 3.58 F
1317 1446 0.792640 CTGAATCTGCCACGTCACAC 59.207 55.000 0.00 0.00 0.00 3.82 F
1356 1485 1.061411 CCATGTTGATGCGACGCTG 59.939 57.895 22.08 8.68 0.00 5.18 F
2139 3139 1.276989 CTGGTGGCTGCCATTTCAATT 59.723 47.619 26.22 0.00 37.96 2.32 F
3117 5894 1.615392 GTCCAGTGGCATTTTTGAGCT 59.385 47.619 3.51 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 3001 0.746659 ACTTGCAAACCTCCAGTTGC 59.253 50.000 0.00 1.51 39.19 4.17 R
3094 5871 0.031857 CAAAAATGCCACTGGACGCA 59.968 50.000 0.00 0.00 39.79 5.24 R
3096 5873 1.666888 GCTCAAAAATGCCACTGGACG 60.667 52.381 0.00 0.00 0.00 4.79 R
3153 5930 5.598417 ACTCAGTTTTGCCACTAGGAATTTT 59.402 36.000 0.00 0.00 36.89 1.82 R
3534 6360 1.335810 CAAACCATGCATCATCGAGGG 59.664 52.381 0.00 0.00 0.00 4.30 R
4721 7867 1.108727 TTGTGGAAAGGGCACTGCAG 61.109 55.000 13.48 13.48 0.00 4.41 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
36 37 1.405526 GGATGTGCTAGCCAGAAACGA 60.406 52.381 13.29 0.00 34.07 3.85
126 132 7.283625 ACTTTTATCTTGTGGTTGCATGTAA 57.716 32.000 0.00 0.00 0.00 2.41
182 188 6.986904 AAGCATTTGTACTAAAGAGCTACC 57.013 37.500 12.58 0.00 0.00 3.18
183 189 6.049955 AGCATTTGTACTAAAGAGCTACCA 57.950 37.500 11.23 0.00 0.00 3.25
184 190 6.109359 AGCATTTGTACTAAAGAGCTACCAG 58.891 40.000 11.23 0.00 0.00 4.00
272 281 3.562505 CACTGAGACTTGAAATGCTTGC 58.437 45.455 0.00 0.00 0.00 4.01
312 321 1.139498 TTTGTGGCAGGGATCAGGGA 61.139 55.000 0.00 0.00 0.00 4.20
430 443 1.293924 CACTCTCCGCAAATAGCTGG 58.706 55.000 0.00 0.00 42.61 4.85
436 449 2.024918 CGCAAATAGCTGGCGGAAT 58.975 52.632 13.72 0.00 46.46 3.01
484 497 1.946768 GCTGAGTTGTACTGTTTGGCA 59.053 47.619 0.00 0.00 0.00 4.92
509 522 1.330306 CAAAATCTTTGCCGAGTGCG 58.670 50.000 0.00 0.00 45.60 5.34
554 567 2.158900 CCTGTTTGCCGGAGAGATGTAT 60.159 50.000 5.05 0.00 0.00 2.29
557 570 1.123077 TTGCCGGAGAGATGTATGCT 58.877 50.000 5.05 0.00 0.00 3.79
656 669 5.147865 CACTCTGCGTATAACTAGATTCCG 58.852 45.833 0.00 0.00 0.00 4.30
660 673 5.764686 TCTGCGTATAACTAGATTCCGGTAA 59.235 40.000 0.00 0.00 0.00 2.85
677 690 9.807921 ATTCCGGTAATGGATCAATATAAAACT 57.192 29.630 0.00 0.00 38.00 2.66
770 785 1.406539 GACGACTAATCCAACGGCCTA 59.593 52.381 0.00 0.00 0.00 3.93
799 814 3.831883 CCTTCGGCATGGATGGTG 58.168 61.111 0.00 0.00 0.00 4.17
800 815 2.484062 CCTTCGGCATGGATGGTGC 61.484 63.158 0.00 0.00 41.78 5.01
801 816 2.823593 TTCGGCATGGATGGTGCG 60.824 61.111 0.00 0.00 43.40 5.34
802 817 3.322318 TTCGGCATGGATGGTGCGA 62.322 57.895 0.00 0.00 43.40 5.10
803 818 2.592574 CGGCATGGATGGTGCGAT 60.593 61.111 0.00 0.00 43.40 4.58
804 819 1.301637 CGGCATGGATGGTGCGATA 60.302 57.895 0.00 0.00 43.40 2.92
805 820 0.674581 CGGCATGGATGGTGCGATAT 60.675 55.000 0.00 0.00 43.40 1.63
806 821 0.806868 GGCATGGATGGTGCGATATG 59.193 55.000 0.00 0.00 43.40 1.78
807 822 1.611410 GGCATGGATGGTGCGATATGA 60.611 52.381 0.00 0.00 43.40 2.15
808 823 2.153645 GCATGGATGGTGCGATATGAA 58.846 47.619 0.00 0.00 32.29 2.57
809 824 2.161012 GCATGGATGGTGCGATATGAAG 59.839 50.000 0.00 0.00 32.29 3.02
810 825 3.405831 CATGGATGGTGCGATATGAAGT 58.594 45.455 0.00 0.00 0.00 3.01
811 826 4.568956 CATGGATGGTGCGATATGAAGTA 58.431 43.478 0.00 0.00 0.00 2.24
812 827 4.890158 TGGATGGTGCGATATGAAGTAT 57.110 40.909 0.00 0.00 0.00 2.12
813 828 5.993748 TGGATGGTGCGATATGAAGTATA 57.006 39.130 0.00 0.00 0.00 1.47
814 829 6.544928 TGGATGGTGCGATATGAAGTATAT 57.455 37.500 0.00 0.00 34.65 0.86
815 830 6.573434 TGGATGGTGCGATATGAAGTATATC 58.427 40.000 0.00 0.00 42.76 1.63
827 842 9.841880 GATATGAAGTATATCGTACTGAAAGCA 57.158 33.333 0.00 0.00 38.59 3.91
854 869 0.609131 AGCACCAATACGCAAAGGCT 60.609 50.000 0.00 0.00 38.10 4.58
993 1017 2.444140 AAGCTAGATCGCCGGGGT 60.444 61.111 19.13 5.83 0.00 4.95
1021 1045 2.325666 GACTCAGCCGCTCGTCTACC 62.326 65.000 10.65 0.00 0.00 3.18
1034 1058 3.214123 CTACCGCCCCGACGATGA 61.214 66.667 0.00 0.00 34.06 2.92
1059 1083 1.716826 CGTCGACTCTAGCCCCTGAC 61.717 65.000 14.70 0.00 0.00 3.51
1070 1094 4.504916 CCCTGACTGCTCGCTCCG 62.505 72.222 0.00 0.00 0.00 4.63
1118 1144 2.609459 AGCTTCGTTTCTAATGGCGATG 59.391 45.455 0.00 0.00 33.27 3.84
1121 1147 2.276201 TCGTTTCTAATGGCGATGGTG 58.724 47.619 0.00 0.00 0.00 4.17
1122 1148 1.268032 CGTTTCTAATGGCGATGGTGC 60.268 52.381 0.00 0.00 0.00 5.01
1159 1185 7.334421 GTGCAGTTAAGAAGGATCTAATGAACA 59.666 37.037 0.00 0.00 33.77 3.18
1216 1242 1.203063 GCCCCTTCCTCTTTTCCACTT 60.203 52.381 0.00 0.00 0.00 3.16
1217 1243 2.041216 GCCCCTTCCTCTTTTCCACTTA 59.959 50.000 0.00 0.00 0.00 2.24
1219 1245 3.348119 CCCTTCCTCTTTTCCACTTAGC 58.652 50.000 0.00 0.00 0.00 3.09
1220 1246 3.244911 CCCTTCCTCTTTTCCACTTAGCA 60.245 47.826 0.00 0.00 0.00 3.49
1222 1248 3.059352 TCCTCTTTTCCACTTAGCAGC 57.941 47.619 0.00 0.00 0.00 5.25
1273 1402 2.009888 GCACTTAGCAGCGATGGAC 58.990 57.895 1.46 0.00 44.79 4.02
1274 1403 1.756375 GCACTTAGCAGCGATGGACG 61.756 60.000 1.46 0.00 44.79 4.79
1276 1405 0.747255 ACTTAGCAGCGATGGACGAT 59.253 50.000 1.46 0.00 45.77 3.73
1313 1442 0.671781 AGCACTGAATCTGCCACGTC 60.672 55.000 0.00 0.00 35.01 4.34
1314 1443 0.950555 GCACTGAATCTGCCACGTCA 60.951 55.000 0.00 0.00 0.00 4.35
1315 1444 0.792640 CACTGAATCTGCCACGTCAC 59.207 55.000 0.00 0.00 0.00 3.67
1316 1445 0.392706 ACTGAATCTGCCACGTCACA 59.607 50.000 0.00 0.00 0.00 3.58
1317 1446 0.792640 CTGAATCTGCCACGTCACAC 59.207 55.000 0.00 0.00 0.00 3.82
1356 1485 1.061411 CCATGTTGATGCGACGCTG 59.939 57.895 22.08 8.68 0.00 5.18
1423 1553 9.803130 CATTTATCTTCAATAAGCTGTCATACG 57.197 33.333 0.00 0.00 32.36 3.06
1480 1715 4.332819 AGTTTGCTATCCAGTAACGAATGC 59.667 41.667 0.00 0.00 0.00 3.56
1492 1727 4.915085 AGTAACGAATGCAATGTTTTTCCG 59.085 37.500 6.85 0.00 0.00 4.30
1516 2504 8.592998 CCGTACTCATCAACACTAGTATTTTTC 58.407 37.037 0.00 0.00 0.00 2.29
1557 2545 2.422597 TGACATGCAGTTTTAGGACCG 58.577 47.619 0.00 0.00 0.00 4.79
1574 2562 2.436539 CGACCGTCGCACTCACATG 61.437 63.158 8.21 0.00 31.14 3.21
1575 2563 2.048222 ACCGTCGCACTCACATGG 60.048 61.111 0.00 0.00 0.00 3.66
1588 2576 2.279741 TCACATGGCTAGATCGTTTGC 58.720 47.619 0.00 0.00 0.00 3.68
1597 2585 2.455674 AGATCGTTTGCAGTGCACTA 57.544 45.000 21.20 6.12 38.71 2.74
1613 2601 3.448660 TGCACTACTCAGCAGACACATAT 59.551 43.478 0.00 0.00 35.51 1.78
1614 2602 4.644685 TGCACTACTCAGCAGACACATATA 59.355 41.667 0.00 0.00 35.51 0.86
1615 2603 5.302823 TGCACTACTCAGCAGACACATATAT 59.697 40.000 0.00 0.00 35.51 0.86
1616 2604 6.490040 TGCACTACTCAGCAGACACATATATA 59.510 38.462 0.00 0.00 35.51 0.86
1669 2657 3.060807 CGTGACAACTTTCGATGAAACGA 60.061 43.478 9.00 0.00 40.55 3.85
1679 2667 6.308282 ACTTTCGATGAAACGATCTAACTGTC 59.692 38.462 0.00 0.00 41.82 3.51
1688 2676 4.021229 ACGATCTAACTGTCCACCACATA 58.979 43.478 0.00 0.00 33.23 2.29
1696 2684 4.072131 ACTGTCCACCACATACACAATTC 58.928 43.478 0.00 0.00 33.23 2.17
1839 2835 5.413969 GCATGCTTGCTTCTTTTCTTTTT 57.586 34.783 16.80 0.00 45.77 1.94
1863 2859 8.561738 TTGTCTTCTATCTTGTTAATTGGTCC 57.438 34.615 0.00 0.00 0.00 4.46
2133 3133 2.008242 TAAAACTGGTGGCTGCCATT 57.992 45.000 26.22 15.91 37.96 3.16
2139 3139 1.276989 CTGGTGGCTGCCATTTCAATT 59.723 47.619 26.22 0.00 37.96 2.32
2506 3554 5.117406 ACAGAGTTCCTCCTTTCAAAAGT 57.883 39.130 2.09 0.00 34.20 2.66
2732 4049 6.016555 ACCCAGTTTTGCCATTAGAAGTTAT 58.983 36.000 0.00 0.00 0.00 1.89
2755 4072 2.749621 ACTCCTCAAAAATGCCATCGTC 59.250 45.455 0.00 0.00 0.00 4.20
2769 4086 2.141517 CATCGTCCCATGAGATGCTTC 58.858 52.381 0.00 0.00 35.89 3.86
2789 4106 4.599047 TCCTCAAAAATGCCATCGTTTT 57.401 36.364 0.00 0.00 41.70 2.43
2869 4186 9.385902 CGTTGACCATGTTATATGATGAAAATC 57.614 33.333 0.00 0.00 0.00 2.17
2893 4210 7.248976 TCCTTCTATACCCACATGTCATCTAT 58.751 38.462 0.00 0.00 0.00 1.98
3019 5796 8.687242 CACACTTTATTGTAGTGAGATAGAGGA 58.313 37.037 9.74 0.00 44.52 3.71
3031 5808 5.767665 GTGAGATAGAGGAAGAGCTGACATA 59.232 44.000 0.00 0.00 0.00 2.29
3089 5866 5.234757 GCAAATGAGATTAGAGAGCTGACAG 59.765 44.000 0.00 0.00 0.00 3.51
3094 5871 7.652524 TGAGATTAGAGAGCTGACAGTAATT 57.347 36.000 3.99 0.00 0.00 1.40
3096 5873 6.279882 AGATTAGAGAGCTGACAGTAATTGC 58.720 40.000 3.99 0.00 0.00 3.56
3117 5894 1.615392 GTCCAGTGGCATTTTTGAGCT 59.385 47.619 3.51 0.00 0.00 4.09
3139 5916 5.950758 TTGTGCCTAACAAAACGATGTAT 57.049 34.783 0.00 0.00 45.85 2.29
3546 6372 4.404073 AGATCCTAATACCCTCGATGATGC 59.596 45.833 0.00 0.00 0.00 3.91
4170 7262 4.530161 CCCAATTCCAAATGTCCCAAACTA 59.470 41.667 0.00 0.00 0.00 2.24
4253 7348 7.384439 TGTGTCTGTTCTGATGTTGTTTTAA 57.616 32.000 0.00 0.00 0.00 1.52
4297 7393 9.529325 AAGCTAAACCTTTATTTGTTCTTCAAC 57.471 29.630 0.00 0.00 35.61 3.18
4388 7484 9.159364 CCATATGTACATTGATAGAACCATGAG 57.841 37.037 14.77 0.00 0.00 2.90
4535 7648 6.268566 TGAGAGTGAATAGACATCATGAACG 58.731 40.000 0.00 0.00 0.00 3.95
4563 7676 6.856494 GTGATACGCACTATCAACTATAGC 57.144 41.667 0.00 0.00 42.47 2.97
4735 7881 1.745653 GGATAACTGCAGTGCCCTTTC 59.254 52.381 22.49 9.05 0.00 2.62
4786 7932 3.431572 GCAAGTCTCAGTTCTGTTAGCTG 59.568 47.826 0.00 0.00 37.75 4.24
4800 7946 7.054491 TCTGTTAGCTGTCATAAGCATATGA 57.946 36.000 6.97 7.54 46.08 2.15
4833 7979 6.552725 AGAATACTTGGATGCTCTCTGATACA 59.447 38.462 0.00 0.00 0.00 2.29
4834 7980 6.931790 ATACTTGGATGCTCTCTGATACAT 57.068 37.500 0.00 0.00 0.00 2.29
5091 10144 9.166173 TCATTCTATAATCTTGGTCAAACACAG 57.834 33.333 0.00 0.00 0.00 3.66
5153 10206 1.137086 CTGGAATGGAGGGAGTACACG 59.863 57.143 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.956199 TCCATCGACTAAACCCGATAAGT 59.044 43.478 0.00 0.00 42.79 2.24
97 99 7.283625 TGCAACCACAAGATAAAAGTAACAT 57.716 32.000 0.00 0.00 0.00 2.71
102 104 5.789643 ACATGCAACCACAAGATAAAAGT 57.210 34.783 0.00 0.00 0.00 2.66
126 132 8.449251 AAACAATAAAGTGGTCAATGCATTTT 57.551 26.923 9.83 2.25 0.00 1.82
160 166 6.049955 TGGTAGCTCTTTAGTACAAATGCT 57.950 37.500 0.00 8.90 0.00 3.79
182 188 5.686159 ACTTCTTTTGAGATGACAAGCTG 57.314 39.130 0.00 0.00 0.00 4.24
183 189 5.049818 CGAACTTCTTTTGAGATGACAAGCT 60.050 40.000 0.00 0.00 0.00 3.74
184 190 5.142962 CGAACTTCTTTTGAGATGACAAGC 58.857 41.667 0.00 0.00 0.00 4.01
190 199 5.657470 TCACACGAACTTCTTTTGAGATG 57.343 39.130 0.00 0.00 0.00 2.90
312 321 5.067805 CCCAGACAACTTTTTACTGCTTTCT 59.932 40.000 0.00 0.00 0.00 2.52
436 449 0.596600 GTGACTTTCACGTCGGCTGA 60.597 55.000 0.00 0.00 37.67 4.26
494 507 1.746615 ATGCGCACTCGGCAAAGAT 60.747 52.632 14.90 0.00 44.66 2.40
509 522 1.239296 TGTTGTGAGCCAGAGCATGC 61.239 55.000 10.51 10.51 43.56 4.06
554 567 1.971167 CGGCAAAAGCCACCTAGCA 60.971 57.895 7.34 0.00 34.23 3.49
557 570 0.605319 CACTCGGCAAAAGCCACCTA 60.605 55.000 7.34 0.00 0.00 3.08
599 612 1.407712 GCAAAGGGCCTATAACCGTCA 60.408 52.381 6.41 0.00 36.11 4.35
638 651 6.384224 CATTACCGGAATCTAGTTATACGCA 58.616 40.000 9.46 0.00 0.00 5.24
656 669 9.232473 GGGAGAGTTTTATATTGATCCATTACC 57.768 37.037 0.00 0.00 0.00 2.85
660 673 7.079451 ACGGGAGAGTTTTATATTGATCCAT 57.921 36.000 0.00 0.00 0.00 3.41
677 690 2.027469 GCCTTTTTCTAGGAACGGGAGA 60.027 50.000 5.59 0.00 37.50 3.71
770 785 1.898574 CCGAAGGCCAAACAGCAGT 60.899 57.895 5.01 0.00 46.14 4.40
801 816 9.841880 TGCTTTCAGTACGATATACTTCATATC 57.158 33.333 0.00 0.00 41.48 1.63
804 819 9.847706 CTATGCTTTCAGTACGATATACTTCAT 57.152 33.333 0.00 0.00 0.00 2.57
805 820 8.847196 ACTATGCTTTCAGTACGATATACTTCA 58.153 33.333 0.00 0.00 0.00 3.02
806 821 9.680315 AACTATGCTTTCAGTACGATATACTTC 57.320 33.333 0.00 0.00 0.00 3.01
807 822 9.680315 GAACTATGCTTTCAGTACGATATACTT 57.320 33.333 0.00 0.00 0.00 2.24
808 823 8.847196 TGAACTATGCTTTCAGTACGATATACT 58.153 33.333 0.00 0.00 0.00 2.12
809 824 9.459640 TTGAACTATGCTTTCAGTACGATATAC 57.540 33.333 0.00 0.00 34.50 1.47
810 825 9.678941 CTTGAACTATGCTTTCAGTACGATATA 57.321 33.333 0.00 0.00 34.50 0.86
811 826 7.169982 GCTTGAACTATGCTTTCAGTACGATAT 59.830 37.037 0.00 0.00 34.50 1.63
812 827 6.475727 GCTTGAACTATGCTTTCAGTACGATA 59.524 38.462 0.00 0.00 34.50 2.92
813 828 5.292101 GCTTGAACTATGCTTTCAGTACGAT 59.708 40.000 0.00 0.00 34.50 3.73
814 829 4.625742 GCTTGAACTATGCTTTCAGTACGA 59.374 41.667 0.00 0.00 34.50 3.43
815 830 4.388773 TGCTTGAACTATGCTTTCAGTACG 59.611 41.667 0.00 0.00 34.50 3.67
816 831 5.390991 GGTGCTTGAACTATGCTTTCAGTAC 60.391 44.000 0.00 0.00 34.50 2.73
817 832 4.695455 GGTGCTTGAACTATGCTTTCAGTA 59.305 41.667 0.00 0.00 34.50 2.74
818 833 3.503748 GGTGCTTGAACTATGCTTTCAGT 59.496 43.478 0.00 0.00 34.50 3.41
819 834 3.503363 TGGTGCTTGAACTATGCTTTCAG 59.497 43.478 0.00 0.00 34.50 3.02
820 835 3.485394 TGGTGCTTGAACTATGCTTTCA 58.515 40.909 0.00 0.00 0.00 2.69
821 836 4.503741 TTGGTGCTTGAACTATGCTTTC 57.496 40.909 0.00 0.00 0.00 2.62
822 837 5.391950 CGTATTGGTGCTTGAACTATGCTTT 60.392 40.000 0.00 0.00 0.00 3.51
823 838 4.094887 CGTATTGGTGCTTGAACTATGCTT 59.905 41.667 0.00 0.00 0.00 3.91
824 839 3.623060 CGTATTGGTGCTTGAACTATGCT 59.377 43.478 0.00 0.00 0.00 3.79
825 840 3.788797 GCGTATTGGTGCTTGAACTATGC 60.789 47.826 0.00 0.00 0.00 3.14
826 841 3.373748 TGCGTATTGGTGCTTGAACTATG 59.626 43.478 0.00 0.00 0.00 2.23
827 842 3.605634 TGCGTATTGGTGCTTGAACTAT 58.394 40.909 0.00 0.00 0.00 2.12
828 843 3.046968 TGCGTATTGGTGCTTGAACTA 57.953 42.857 0.00 0.00 0.00 2.24
829 844 1.890876 TGCGTATTGGTGCTTGAACT 58.109 45.000 0.00 0.00 0.00 3.01
854 869 3.319198 GGCCTGGACTCGGGTGAA 61.319 66.667 0.00 0.00 41.53 3.18
971 995 2.663188 GGCGATCTAGCTTGCCCG 60.663 66.667 13.15 0.00 39.46 6.13
972 996 2.663188 CGGCGATCTAGCTTGCCC 60.663 66.667 17.46 2.52 41.97 5.36
973 997 2.663188 CCGGCGATCTAGCTTGCC 60.663 66.667 14.01 14.01 41.61 4.52
974 998 2.663188 CCCGGCGATCTAGCTTGC 60.663 66.667 9.30 0.00 37.29 4.01
975 999 2.029666 CCCCGGCGATCTAGCTTG 59.970 66.667 9.30 0.00 37.29 4.01
993 1017 1.078918 CGGCTGAGTCATGGCTCAA 60.079 57.895 28.75 14.09 43.92 3.02
1034 1058 1.086634 GGCTAGAGTCGACGTACGGT 61.087 60.000 21.06 5.07 42.82 4.83
1070 1094 2.434359 CAGAGGGGAACGAACGCC 60.434 66.667 10.42 10.42 42.13 5.68
1097 1123 2.380084 TCGCCATTAGAAACGAAGCT 57.620 45.000 0.00 0.00 0.00 3.74
1216 1242 3.086818 TGTAACGCATTATCGCTGCTA 57.913 42.857 0.00 0.00 37.48 3.49
1217 1243 1.934589 TGTAACGCATTATCGCTGCT 58.065 45.000 0.00 0.00 37.48 4.24
1219 1245 3.997276 TGTTTGTAACGCATTATCGCTG 58.003 40.909 0.00 0.00 0.00 5.18
1220 1246 4.875544 ATGTTTGTAACGCATTATCGCT 57.124 36.364 0.00 0.00 0.00 4.93
1222 1248 5.050363 AGCCTATGTTTGTAACGCATTATCG 60.050 40.000 0.00 0.00 0.00 2.92
1268 1397 6.949352 ATTCAAGCAAATCTAATCGTCCAT 57.051 33.333 0.00 0.00 0.00 3.41
1313 1442 5.746245 ACCAAAACAAAATCATACACGTGTG 59.254 36.000 30.83 15.50 0.00 3.82
1314 1443 5.897050 ACCAAAACAAAATCATACACGTGT 58.103 33.333 26.52 26.52 0.00 4.49
1315 1444 5.401079 GGACCAAAACAAAATCATACACGTG 59.599 40.000 15.48 15.48 0.00 4.49
1316 1445 5.067936 TGGACCAAAACAAAATCATACACGT 59.932 36.000 0.00 0.00 0.00 4.49
1317 1446 5.524284 TGGACCAAAACAAAATCATACACG 58.476 37.500 0.00 0.00 0.00 4.49
1318 1447 6.928492 ACATGGACCAAAACAAAATCATACAC 59.072 34.615 0.00 0.00 0.00 2.90
1319 1448 7.060383 ACATGGACCAAAACAAAATCATACA 57.940 32.000 0.00 0.00 0.00 2.29
1356 1485 5.175856 CCGCTGTAACTATGCAAGATAACTC 59.824 44.000 0.00 0.00 0.00 3.01
1423 1553 6.481954 AAACATTCGACCAGAACTATGTTC 57.518 37.500 7.96 2.54 42.39 3.18
1480 1715 6.359617 GTGTTGATGAGTACGGAAAAACATTG 59.640 38.462 8.86 0.00 0.00 2.82
1516 2504 1.340308 TGGACTCATGGTTGCCATCAG 60.340 52.381 0.00 0.00 43.15 2.90
1557 2545 2.094659 CCATGTGAGTGCGACGGTC 61.095 63.158 0.00 0.00 0.00 4.79
1574 2562 0.375106 GCACTGCAAACGATCTAGCC 59.625 55.000 0.00 0.00 0.00 3.93
1575 2563 1.078709 TGCACTGCAAACGATCTAGC 58.921 50.000 0.00 0.00 34.76 3.42
1588 2576 1.000171 TGTCTGCTGAGTAGTGCACTG 60.000 52.381 29.57 13.13 37.72 3.66
1597 2585 8.870075 TCTATGTATATATGTGTCTGCTGAGT 57.130 34.615 0.00 0.00 0.00 3.41
1614 2602 9.011095 CCATGATTTTTCAGCTGATCTATGTAT 57.989 33.333 19.04 4.73 0.00 2.29
1615 2603 7.994911 ACCATGATTTTTCAGCTGATCTATGTA 59.005 33.333 19.04 0.00 0.00 2.29
1616 2604 6.832384 ACCATGATTTTTCAGCTGATCTATGT 59.168 34.615 19.04 7.51 0.00 2.29
1669 2657 4.530553 TGTGTATGTGGTGGACAGTTAGAT 59.469 41.667 0.00 0.00 38.23 1.98
1679 2667 5.647658 ACACTATGAATTGTGTATGTGGTGG 59.352 40.000 8.46 0.00 43.11 4.61
1688 2676 9.026121 AGAGTACTTCTACACTATGAATTGTGT 57.974 33.333 13.60 13.60 45.82 3.72
1696 2684 9.837525 AACGTTTTAGAGTACTTCTACACTATG 57.162 33.333 0.00 0.00 38.12 2.23
1703 2691 8.931385 AAACACAACGTTTTAGAGTACTTCTA 57.069 30.769 0.00 0.00 45.79 2.10
1718 2706 7.030165 TGAAAATACATGACAAAACACAACGT 58.970 30.769 0.00 0.00 0.00 3.99
1839 2835 7.685481 TGGACCAATTAACAAGATAGAAGACA 58.315 34.615 0.00 0.00 0.00 3.41
1928 2925 1.304134 GCCGATGGGTCACCCTTTT 60.304 57.895 16.04 0.00 45.70 2.27
2004 3001 0.746659 ACTTGCAAACCTCCAGTTGC 59.253 50.000 0.00 1.51 39.19 4.17
2133 3133 7.812690 AGATGTCATGCTAGCAATAATTGAA 57.187 32.000 23.54 11.10 0.00 2.69
2139 3139 7.065443 GCAATCATAGATGTCATGCTAGCAATA 59.935 37.037 23.54 10.04 32.91 1.90
2506 3554 6.682113 GCCATAGTTTATGTCGACTGGAACTA 60.682 42.308 25.53 25.53 35.03 2.24
2732 4049 4.331968 ACGATGGCATTTTTGAGGAGTTA 58.668 39.130 0.00 0.00 0.00 2.24
2755 4072 2.723322 TTGAGGAAGCATCTCATGGG 57.277 50.000 4.85 0.00 40.46 4.00
2769 4086 4.057432 ACAAAACGATGGCATTTTTGAGG 58.943 39.130 29.99 14.13 40.96 3.86
2789 4106 7.946207 TGGCATTTTTGAGTAAACATCTAACA 58.054 30.769 0.00 0.00 0.00 2.41
2823 4140 4.957296 ACGAGTTTGACCTGACAATAACT 58.043 39.130 0.00 0.00 0.00 2.24
2869 4186 5.815233 AGATGACATGTGGGTATAGAAGG 57.185 43.478 1.15 0.00 0.00 3.46
3019 5796 6.265649 ACGTATAGACCAATATGTCAGCTCTT 59.734 38.462 0.00 0.00 37.73 2.85
3031 5808 8.974060 AATGACCAAAATACGTATAGACCAAT 57.026 30.769 8.83 0.00 0.00 3.16
3070 5847 7.487484 CAATTACTGTCAGCTCTCTAATCTCA 58.513 38.462 0.00 0.00 0.00 3.27
3077 5854 2.232452 ACGCAATTACTGTCAGCTCTCT 59.768 45.455 0.00 0.00 0.00 3.10
3078 5855 2.600867 GACGCAATTACTGTCAGCTCTC 59.399 50.000 0.00 0.00 32.91 3.20
3079 5856 2.611518 GACGCAATTACTGTCAGCTCT 58.388 47.619 0.00 0.00 32.91 4.09
3089 5866 1.094785 ATGCCACTGGACGCAATTAC 58.905 50.000 0.00 0.00 38.75 1.89
3094 5871 0.031857 CAAAAATGCCACTGGACGCA 59.968 50.000 0.00 0.00 39.79 5.24
3096 5873 1.666888 GCTCAAAAATGCCACTGGACG 60.667 52.381 0.00 0.00 0.00 4.79
3117 5894 5.950758 ATACATCGTTTTGTTAGGCACAA 57.049 34.783 0.00 0.00 44.11 3.33
3153 5930 5.598417 ACTCAGTTTTGCCACTAGGAATTTT 59.402 36.000 0.00 0.00 36.89 1.82
3534 6360 1.335810 CAAACCATGCATCATCGAGGG 59.664 52.381 0.00 0.00 0.00 4.30
3537 6363 5.833406 AAATACAAACCATGCATCATCGA 57.167 34.783 0.00 0.00 0.00 3.59
4044 7132 6.626302 TGACCAACAAAAGAAAAGGTAACAG 58.374 36.000 0.00 0.00 41.41 3.16
4059 7151 1.847737 ACCTACCCAACTGACCAACAA 59.152 47.619 0.00 0.00 0.00 2.83
4170 7262 4.484912 AGAAACTACTCCCTCAACACTCT 58.515 43.478 0.00 0.00 0.00 3.24
4455 7564 6.283544 AGTTAGGTTTTCTAGGCTAGTCAC 57.716 41.667 20.45 14.56 0.00 3.67
4535 7648 5.043903 AGTTGATAGTGCGTATCACACATC 58.956 41.667 7.85 1.46 46.06 3.06
4721 7867 1.108727 TTGTGGAAAGGGCACTGCAG 61.109 55.000 13.48 13.48 0.00 4.41
4786 7932 9.650539 ATTCTCTACACATCATATGCTTATGAC 57.349 33.333 20.94 0.00 45.29 3.06
4800 7946 6.326064 AGAGCATCCAAGTATTCTCTACACAT 59.674 38.462 0.00 0.00 33.66 3.21
4814 7960 5.211174 TCATGTATCAGAGAGCATCCAAG 57.789 43.478 0.00 0.00 33.66 3.61
4833 7979 7.859540 ACTATGAGCCATATCTAAGCATTCAT 58.140 34.615 0.00 0.00 0.00 2.57
4834 7980 7.250032 ACTATGAGCCATATCTAAGCATTCA 57.750 36.000 0.00 0.00 0.00 2.57
5063 9669 9.994432 GTGTTTGACCAAGATTATAGAATGAAG 57.006 33.333 0.00 0.00 0.00 3.02
5153 10206 3.254629 ACACCCTGCACATGATGTC 57.745 52.632 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.