Multiple sequence alignment - TraesCS6D01G110100

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 TraesCS6D01G110100 chr6D 100.000 5787 0 0 1 5787 75875054 75869268 0.000000e+00 10687.0
1 TraesCS6D01G110100 chr6D 76.692 1300 279 20 2031 3318 14934408 14935695 0.000000e+00 701.0
2 TraesCS6D01G110100 chr6D 76.954 1228 246 29 2025 3233 75756568 75755359 0.000000e+00 665.0
3 TraesCS6D01G110100 chr6D 90.043 462 40 4 5332 5787 75766880 75766419 1.390000e-165 593.0
4 TraesCS6D01G110100 chr6D 96.753 154 5 0 426 579 75874783 75874630 2.070000e-64 257.0
5 TraesCS6D01G110100 chr6D 78.158 380 83 0 5404 5783 14497102 14496723 5.790000e-60 243.0
6 TraesCS6D01G110100 chr6D 78.552 373 74 4 5419 5785 438839536 438839164 2.080000e-59 241.0
7 TraesCS6D01G110100 chr6D 78.502 307 63 3 5419 5724 14900538 14900842 1.270000e-46 198.0
8 TraesCS6D01G110100 chr6B 94.446 3547 149 19 606 4126 149472956 149469432 0.000000e+00 5415.0
9 TraesCS6D01G110100 chr6B 89.906 1387 97 22 4424 5787 149469175 149467809 0.000000e+00 1746.0
10 TraesCS6D01G110100 chr6B 87.659 786 40 13 5030 5787 149434162 149433406 0.000000e+00 861.0
11 TraesCS6D01G110100 chr6B 90.747 616 52 4 3567 4182 149440871 149440261 0.000000e+00 817.0
12 TraesCS6D01G110100 chr6B 77.890 1090 225 14 2026 3107 26487006 26485925 0.000000e+00 664.0
13 TraesCS6D01G110100 chr6B 87.648 591 35 17 4457 5044 149434864 149434309 0.000000e+00 652.0
14 TraesCS6D01G110100 chr6B 79.255 376 70 6 5419 5787 664070380 664070006 7.440000e-64 255.0
15 TraesCS6D01G110100 chr6B 92.683 82 4 2 4175 4256 149440235 149440156 3.660000e-22 117.0
16 TraesCS6D01G110100 chr6B 97.727 44 1 0 4175 4218 149469308 149469265 6.220000e-10 76.8
17 TraesCS6D01G110100 chr6A 96.218 2221 55 9 1960 4180 91886019 91883828 0.000000e+00 3609.0
18 TraesCS6D01G110100 chr6A 91.878 1379 77 17 603 1961 91887486 91886123 0.000000e+00 1893.0
19 TraesCS6D01G110100 chr6A 90.859 1280 63 34 4510 5787 91883311 91882084 0.000000e+00 1666.0
20 TraesCS6D01G110100 chr6A 78.359 1109 228 12 2026 3128 15654924 15653822 0.000000e+00 708.0
21 TraesCS6D01G110100 chr6A 91.457 398 24 5 4184 4577 91883705 91883314 6.600000e-149 538.0
22 TraesCS6D01G110100 chr6A 75.985 812 182 13 1021 1825 15656124 15655319 1.940000e-109 407.0
23 TraesCS6D01G110100 chr6A 80.902 377 62 7 5419 5787 587698581 587698207 7.340000e-74 289.0
24 TraesCS6D01G110100 chr6A 79.370 349 72 0 5420 5768 15656111 15655763 4.480000e-61 246.0
25 TraesCS6D01G110100 chr5B 95.059 425 21 0 4 428 271150082 271149658 0.000000e+00 669.0
26 TraesCS6D01G110100 chr5B 94.824 425 22 0 4 428 479813810 479813386 0.000000e+00 664.0
27 TraesCS6D01G110100 chr5B 94.353 425 24 0 4 428 368804419 368803995 0.000000e+00 652.0
28 TraesCS6D01G110100 chr5B 95.455 154 7 0 426 579 479812510 479812357 4.480000e-61 246.0
29 TraesCS6D01G110100 chr5B 94.340 159 8 1 426 583 271149469 271149311 5.790000e-60 243.0
30 TraesCS6D01G110100 chr5B 94.805 154 8 0 426 579 368803806 368803653 2.080000e-59 241.0
31 TraesCS6D01G110100 chr5B 73.832 321 71 12 2024 2338 477981100 477980787 1.320000e-21 115.0
32 TraesCS6D01G110100 chr4A 94.432 431 24 0 1 431 609551959 609552389 0.000000e+00 664.0
33 TraesCS6D01G110100 chr4A 77.439 820 168 14 2026 2836 729706908 729707719 1.890000e-129 473.0
34 TraesCS6D01G110100 chr1A 94.824 425 22 0 4 428 148614245 148613821 0.000000e+00 664.0
35 TraesCS6D01G110100 chr1A 94.379 427 22 1 1 425 521850947 521851373 0.000000e+00 654.0
36 TraesCS6D01G110100 chr1A 93.692 428 27 0 1 428 61119104 61119531 4.890000e-180 641.0
37 TraesCS6D01G110100 chr1A 93.671 158 10 0 426 583 521851220 521851377 2.700000e-58 237.0
38 TraesCS6D01G110100 chr1A 78.108 370 72 7 5420 5783 586519848 586519482 5.830000e-55 226.0
39 TraesCS6D01G110100 chr1A 78.723 282 60 0 5420 5701 586411724 586411443 7.660000e-44 189.0
40 TraesCS6D01G110100 chr7A 94.118 425 25 0 4 428 731815918 731815494 0.000000e+00 647.0
41 TraesCS6D01G110100 chr7A 95.455 154 7 0 426 579 731814618 731814465 4.480000e-61 246.0
42 TraesCS6D01G110100 chr2A 93.882 425 26 0 4 428 6156647 6156223 4.890000e-180 641.0
43 TraesCS6D01G110100 chr1D 74.706 680 157 11 1018 1691 487897346 487896676 7.340000e-74 289.0
44 TraesCS6D01G110100 chrUn 74.174 666 153 15 1034 1691 8846012 8845358 5.750000e-65 259.0
45 TraesCS6D01G110100 chrUn 95.455 154 7 0 426 579 290007169 290007016 4.480000e-61 246.0
46 TraesCS6D01G110100 chrUn 94.805 154 8 0 426 579 288970097 288970250 2.080000e-59 241.0
47 TraesCS6D01G110100 chr5D 91.667 168 14 0 426 593 539030909 539031076 3.490000e-57 233.0
48 TraesCS6D01G110100 chr5D 89.080 174 15 3 4177 4346 356846044 356845871 4.540000e-51 213.0
49 TraesCS6D01G110100 chr5D 70.404 767 179 39 2024 2762 397937725 397936979 1.320000e-21 115.0
50 TraesCS6D01G110100 chr1B 77.236 369 75 6 5420 5782 679710549 679710184 2.110000e-49 207.0
51 TraesCS6D01G110100 chr1B 94.595 37 2 0 3754 3790 673861752 673861716 2.250000e-04 58.4
52 TraesCS6D01G110100 chr5A 73.750 320 73 11 2024 2338 503057858 503057545 1.320000e-21 115.0


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 TraesCS6D01G110100 chr6D 75869268 75875054 5786 True 5472.000000 10687 98.376500 1 5787 2 chr6D.!!$R5 5786
1 TraesCS6D01G110100 chr6D 14934408 14935695 1287 False 701.000000 701 76.692000 2031 3318 1 chr6D.!!$F2 1287
2 TraesCS6D01G110100 chr6D 75755359 75756568 1209 True 665.000000 665 76.954000 2025 3233 1 chr6D.!!$R2 1208
3 TraesCS6D01G110100 chr6B 149467809 149472956 5147 True 2412.600000 5415 94.026333 606 5787 3 chr6B.!!$R5 5181
4 TraesCS6D01G110100 chr6B 149433406 149434864 1458 True 756.500000 861 87.653500 4457 5787 2 chr6B.!!$R3 1330
5 TraesCS6D01G110100 chr6B 26485925 26487006 1081 True 664.000000 664 77.890000 2026 3107 1 chr6B.!!$R1 1081
6 TraesCS6D01G110100 chr6B 149440156 149440871 715 True 467.000000 817 91.715000 3567 4256 2 chr6B.!!$R4 689
7 TraesCS6D01G110100 chr6A 91882084 91887486 5402 True 1926.500000 3609 92.603000 603 5787 4 chr6A.!!$R3 5184
8 TraesCS6D01G110100 chr6A 15653822 15656124 2302 True 453.666667 708 77.904667 1021 5768 3 chr6A.!!$R2 4747
9 TraesCS6D01G110100 chr5B 271149311 271150082 771 True 456.000000 669 94.699500 4 583 2 chr5B.!!$R2 579
10 TraesCS6D01G110100 chr5B 479812357 479813810 1453 True 455.000000 664 95.139500 4 579 2 chr5B.!!$R4 575
11 TraesCS6D01G110100 chr5B 368803653 368804419 766 True 446.500000 652 94.579000 4 579 2 chr5B.!!$R3 575
12 TraesCS6D01G110100 chr4A 729706908 729707719 811 False 473.000000 473 77.439000 2026 2836 1 chr4A.!!$F2 810
13 TraesCS6D01G110100 chr7A 731814465 731815918 1453 True 446.500000 647 94.786500 4 579 2 chr7A.!!$R1 575
14 TraesCS6D01G110100 chr1D 487896676 487897346 670 True 289.000000 289 74.706000 1018 1691 1 chr1D.!!$R1 673
15 TraesCS6D01G110100 chrUn 8845358 8846012 654 True 259.000000 259 74.174000 1034 1691 1 chrUn.!!$R1 657

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
851 2419 0.252012 CCAGTCTCCACCTCCTGAGT 60.252 60.000 0.0 0.0 0.00 3.41 F
852 2420 1.006043 CCAGTCTCCACCTCCTGAGTA 59.994 57.143 0.0 0.0 0.00 2.59 F
1844 3419 0.179156 CGCTGCACTTTTATGGGCTG 60.179 55.000 0.0 0.0 0.00 4.85 F
2164 3972 1.985159 ACTAGGTGATGTGGCTTTCCA 59.015 47.619 0.0 0.0 40.85 3.53 F
3650 5466 1.869767 CTCAGTCTCAAGGTGTTGTGC 59.130 52.381 0.0 0.0 34.98 4.57 F
3932 5757 0.990374 AGTCTGCCTTCAGGAATGCT 59.010 50.000 10.0 0.0 40.69 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3400 0.179156 CAGCCCATAAAAGTGCAGCG 60.179 55.000 0.00 0.0 0.00 5.18 R
2415 4223 0.463620 GGCTTTGTGGCAAACTTGGA 59.536 50.000 0.00 0.0 41.37 3.53 R
3432 5248 2.609459 CCAGCAGGTCGACATAATGTTC 59.391 50.000 18.91 0.0 0.00 3.18 R
3904 5728 1.827344 TGAAGGCAGACTCGACATCAT 59.173 47.619 0.00 0.0 0.00 2.45 R
4635 6710 0.592637 TGCAAGCAATTGAGTGGTCG 59.407 50.000 10.34 0.0 0.00 4.79 R
4992 7077 1.338579 GCCTGGTCACTCTCAGAAAGG 60.339 57.143 0.00 0.0 33.11 3.11 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
26 27 4.019858 TGGGAGAGATATGATCGTGATCC 58.980 47.826 7.36 0.00 37.02 3.36
32 33 4.928263 AGATATGATCGTGATCCAGGAGA 58.072 43.478 7.36 0.00 37.02 3.71
47 48 2.502947 CAGGAGATCAAGGTGATGGACA 59.497 50.000 0.00 0.00 37.20 4.02
164 165 3.782046 ACAGGATCGTGATTAGTTTCCG 58.218 45.455 21.63 0.00 0.00 4.30
172 173 5.159209 TCGTGATTAGTTTCCGAAGAAGAC 58.841 41.667 0.00 0.00 32.35 3.01
178 179 3.991367 AGTTTCCGAAGAAGACGTGATT 58.009 40.909 0.00 0.00 32.35 2.57
206 207 4.189639 AGTTTCCTAAGAAGACGCGATT 57.810 40.909 15.93 7.15 32.35 3.34
258 259 4.264253 TGGAGTTTCATATGGTGAAGCAG 58.736 43.478 2.13 0.00 46.77 4.24
318 319 3.776417 TGGATTAGGTTAAGGTTAGCCGT 59.224 43.478 0.00 0.00 38.83 5.68
361 362 7.086376 GCTTAATCATGCGGTCATAATGAATT 58.914 34.615 0.00 0.00 34.21 2.17
375 376 9.191376 GTCATAATGAATTCGTGTACGTTTTAC 57.809 33.333 0.00 0.00 40.80 2.01
389 390 2.225963 CGTTTTACGGGGTGCATGTAAA 59.774 45.455 10.53 10.53 38.08 2.01
484 2050 4.946445 AGGCTAGCCGTTAGATTAAGTTC 58.054 43.478 27.83 0.00 41.95 3.01
515 2081 7.086376 GCTTAATCATGCGGTCATAATGAATT 58.914 34.615 0.00 0.00 34.21 2.17
523 2089 4.318546 GCGGTCATAATGAATTCGTGTACC 60.319 45.833 0.00 6.03 0.00 3.34
538 2104 3.361786 GTGTACCTTTTATGGGGTGCAT 58.638 45.455 6.23 0.00 46.41 3.96
543 2109 4.421131 ACCTTTTATGGGGTGCATGTAAA 58.579 39.130 0.00 0.00 34.16 2.01
545 2111 5.487131 ACCTTTTATGGGGTGCATGTAAAAT 59.513 36.000 0.00 0.00 34.16 1.82
590 2156 8.830915 AATAGTAGTGGAGAAGAAGATGAAGA 57.169 34.615 0.00 0.00 0.00 2.87
591 2157 9.432982 AATAGTAGTGGAGAAGAAGATGAAGAT 57.567 33.333 0.00 0.00 0.00 2.40
592 2158 7.111247 AGTAGTGGAGAAGAAGATGAAGATG 57.889 40.000 0.00 0.00 0.00 2.90
593 2159 5.356291 AGTGGAGAAGAAGATGAAGATGG 57.644 43.478 0.00 0.00 0.00 3.51
594 2160 5.028802 AGTGGAGAAGAAGATGAAGATGGA 58.971 41.667 0.00 0.00 0.00 3.41
595 2161 5.486775 AGTGGAGAAGAAGATGAAGATGGAA 59.513 40.000 0.00 0.00 0.00 3.53
596 2162 5.816777 GTGGAGAAGAAGATGAAGATGGAAG 59.183 44.000 0.00 0.00 0.00 3.46
597 2163 5.486775 TGGAGAAGAAGATGAAGATGGAAGT 59.513 40.000 0.00 0.00 0.00 3.01
598 2164 5.816777 GGAGAAGAAGATGAAGATGGAAGTG 59.183 44.000 0.00 0.00 0.00 3.16
599 2165 5.743117 AGAAGAAGATGAAGATGGAAGTGG 58.257 41.667 0.00 0.00 0.00 4.00
600 2166 5.486775 AGAAGAAGATGAAGATGGAAGTGGA 59.513 40.000 0.00 0.00 0.00 4.02
601 2167 5.356291 AGAAGATGAAGATGGAAGTGGAG 57.644 43.478 0.00 0.00 0.00 3.86
632 2198 0.730834 CCAGACGCGTCTCTGACTTG 60.731 60.000 37.41 24.38 40.28 3.16
633 2199 0.730834 CAGACGCGTCTCTGACTTGG 60.731 60.000 37.41 20.37 40.28 3.61
651 2217 0.999712 GGTCCTTCTCCCCCAAATCA 59.000 55.000 0.00 0.00 0.00 2.57
658 2224 0.630673 CTCCCCCAAATCACATCCCA 59.369 55.000 0.00 0.00 0.00 4.37
661 2227 1.568597 CCCCCAAATCACATCCCACTA 59.431 52.381 0.00 0.00 0.00 2.74
670 2236 1.227380 CATCCCACTACTGCTCCGC 60.227 63.158 0.00 0.00 0.00 5.54
671 2237 2.786495 ATCCCACTACTGCTCCGCG 61.786 63.158 0.00 0.00 0.00 6.46
851 2419 0.252012 CCAGTCTCCACCTCCTGAGT 60.252 60.000 0.00 0.00 0.00 3.41
852 2420 1.006043 CCAGTCTCCACCTCCTGAGTA 59.994 57.143 0.00 0.00 0.00 2.59
916 2484 2.001361 AATCGCCGTCCTCTACACCG 62.001 60.000 0.00 0.00 0.00 4.94
922 2490 1.380112 GTCCTCTACACCGCCTCCT 60.380 63.158 0.00 0.00 0.00 3.69
1044 2618 1.542547 GCGACGATGGGGGTAATGAAT 60.543 52.381 0.00 0.00 0.00 2.57
1392 2966 2.124778 GCTCTTGCTCTGGAGGCC 60.125 66.667 0.00 0.00 36.03 5.19
1419 2993 2.120232 CGACGCATGAGGTACAAGATC 58.880 52.381 0.00 0.00 0.00 2.75
1423 2997 2.479560 CGCATGAGGTACAAGATCGACA 60.480 50.000 0.00 0.00 0.00 4.35
1444 3018 5.931532 ACAATTGCGTTGATTCTAGTTCTG 58.068 37.500 5.05 0.00 40.37 3.02
1466 3040 2.966732 TTGTGCCTGTCGATCCCCC 61.967 63.158 0.00 0.00 0.00 5.40
1473 3047 1.279271 CCTGTCGATCCCCCAATATCC 59.721 57.143 0.00 0.00 0.00 2.59
1558 3132 7.173218 TCAGTTGGTTGATTGATACTGAGAAAC 59.827 37.037 0.00 0.00 37.62 2.78
1844 3419 0.179156 CGCTGCACTTTTATGGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
1951 3569 5.481473 ACTTATTGGCCATGAAATGTTCAGT 59.519 36.000 6.09 0.00 44.81 3.41
2164 3972 1.985159 ACTAGGTGATGTGGCTTTCCA 59.015 47.619 0.00 0.00 40.85 3.53
2315 4123 5.284079 TCAGCTGAAATTTTGAAGAAGTGC 58.716 37.500 15.67 0.00 0.00 4.40
2415 4223 2.776536 AGCATAAGGGATTCACTGAGCT 59.223 45.455 4.67 4.67 0.00 4.09
3053 4869 6.543735 ACTTAGGTATTTGAAGGTTTCAGCT 58.456 36.000 0.00 0.00 41.38 4.24
3432 5248 2.681848 CTCTACCTTGCCTGCAATCTTG 59.318 50.000 4.84 0.00 35.20 3.02
3650 5466 1.869767 CTCAGTCTCAAGGTGTTGTGC 59.130 52.381 0.00 0.00 34.98 4.57
3664 5480 3.066621 GTGTTGTGCATTCCTCAAGACAA 59.933 43.478 8.75 0.00 39.56 3.18
3860 5684 3.624777 CATGGTGCAACTCTTATCCCTT 58.375 45.455 2.04 0.00 36.74 3.95
3904 5728 1.138859 GTCATCCATCCATGACGACCA 59.861 52.381 0.00 0.00 42.48 4.02
3929 5753 1.205893 GTCGAGTCTGCCTTCAGGAAT 59.794 52.381 0.00 0.00 40.69 3.01
3932 5757 0.990374 AGTCTGCCTTCAGGAATGCT 59.010 50.000 10.00 0.00 40.69 3.79
3956 5781 3.070576 GTGCACCCAAGATGCCCC 61.071 66.667 5.22 0.00 42.69 5.80
3958 5783 4.380945 GCACCCAAGATGCCCCCA 62.381 66.667 0.00 0.00 37.08 4.96
4009 5834 8.325787 TGATTGGCCTTCTCTGTAACTTAAATA 58.674 33.333 3.32 0.00 0.00 1.40
4072 5898 2.631418 TTACTGTGTACGAGCTCTGC 57.369 50.000 12.85 3.37 0.00 4.26
4131 5957 7.418337 TGTCAGAGTTAGTATATTTGGCTGA 57.582 36.000 0.00 0.00 0.00 4.26
4180 6167 3.315470 CAGTTCCTGCATGATCTGAATGG 59.685 47.826 19.61 0.13 35.15 3.16
4289 6278 6.009908 TCCTGATCATTGATGTTTGAGGAT 57.990 37.500 3.32 0.00 0.00 3.24
4329 6318 4.355543 TTTGATTAATCTTCTGCGCCAC 57.644 40.909 16.24 0.00 0.00 5.01
4366 6356 4.520492 CACTAGCTGTTTCCTTTCCAATGT 59.480 41.667 0.00 0.00 0.00 2.71
4372 6362 5.523438 TGTTTCCTTTCCAATGTGTAACC 57.477 39.130 0.00 0.00 34.36 2.85
4402 6392 5.588648 GTCCTACAAAATATGCAAGCCTACA 59.411 40.000 0.00 0.00 0.00 2.74
4406 6396 4.104776 CAAAATATGCAAGCCTACAACCG 58.895 43.478 0.00 0.00 0.00 4.44
4407 6397 2.710096 ATATGCAAGCCTACAACCGT 57.290 45.000 0.00 0.00 0.00 4.83
4415 6405 2.532843 AGCCTACAACCGTTCCTTAGA 58.467 47.619 0.00 0.00 0.00 2.10
4480 6476 6.655003 GGAGTGTAATTCAGAAATCAGAACCA 59.345 38.462 0.00 0.00 0.00 3.67
4525 6529 6.314896 CGGCATTCTGAAGAGAGATAAAAACT 59.685 38.462 0.00 0.00 0.00 2.66
4537 6541 5.301805 AGAGATAAAAACTGGTGGTGGTTTG 59.698 40.000 0.00 0.00 36.06 2.93
4541 6545 1.585651 AACTGGTGGTGGTTTGGGGA 61.586 55.000 0.00 0.00 0.00 4.81
4560 6635 4.761227 GGGGACTCTACTTTATCTACGGAG 59.239 50.000 0.00 0.00 0.00 4.63
4635 6710 4.044426 CAGTAGCACAAAAGCTTTGTTCC 58.956 43.478 13.54 2.39 43.70 3.62
4646 6721 1.880027 GCTTTGTTCCGACCACTCAAT 59.120 47.619 0.00 0.00 0.00 2.57
4660 6735 3.250744 CACTCAATTGCTTGCAATCCTG 58.749 45.455 19.32 15.08 32.11 3.86
4757 6835 1.808891 CGACCTCACTCAACCGGTTTT 60.809 52.381 19.55 1.43 0.00 2.43
4773 6851 2.619646 GGTTTTTCTCCGGCTGTTGTTA 59.380 45.455 0.00 0.00 0.00 2.41
4804 6882 6.238842 CCAGATGACAATGGTGATGTTAATCC 60.239 42.308 2.55 0.00 30.47 3.01
4837 6915 1.266989 CCCCTTTGTTCGAGTCTTTGC 59.733 52.381 0.00 0.00 0.00 3.68
4902 6980 1.901948 TCTCCGGCTGTCGTTGTCT 60.902 57.895 0.00 0.00 37.11 3.41
4992 7077 1.281899 CGGAATCGTCTTCTTGGCTC 58.718 55.000 0.00 0.00 0.00 4.70
5024 7109 0.175760 GACCAGGCATCAGCTTCGTA 59.824 55.000 0.00 0.00 41.70 3.43
5025 7110 0.108138 ACCAGGCATCAGCTTCGTAC 60.108 55.000 0.00 0.00 41.70 3.67
5026 7111 1.148157 CCAGGCATCAGCTTCGTACG 61.148 60.000 9.53 9.53 41.70 3.67
5027 7112 0.458543 CAGGCATCAGCTTCGTACGT 60.459 55.000 16.05 0.00 41.70 3.57
5028 7113 1.100510 AGGCATCAGCTTCGTACGTA 58.899 50.000 16.05 4.53 41.70 3.57
5029 7114 1.197910 GGCATCAGCTTCGTACGTAC 58.802 55.000 15.90 15.90 41.70 3.67
5059 7307 1.471119 ATGGATTCACAGCCTTGCAG 58.529 50.000 0.00 0.00 0.00 4.41
5100 7351 2.097444 CCACGCTGAATTTTCAAAACGC 60.097 45.455 8.89 2.48 36.64 4.84
5261 7518 0.324738 ATCCACCTCTTGAGCTCCGA 60.325 55.000 12.15 6.95 0.00 4.55
5439 7721 1.415672 GGGCGATGAACCCCCTCATA 61.416 60.000 0.00 0.00 42.01 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.649218 TCACGATCATATCTCTCCCAACAA 59.351 41.667 0.00 0.00 0.00 2.83
1 2 4.215109 TCACGATCATATCTCTCCCAACA 58.785 43.478 0.00 0.00 0.00 3.33
2 3 4.855715 TCACGATCATATCTCTCCCAAC 57.144 45.455 0.00 0.00 0.00 3.77
26 27 2.502947 TGTCCATCACCTTGATCTCCTG 59.497 50.000 0.00 0.00 34.28 3.86
32 33 4.305539 TTGACATGTCCATCACCTTGAT 57.694 40.909 22.85 0.00 37.65 2.57
35 36 3.760151 CACATTGACATGTCCATCACCTT 59.240 43.478 22.85 0.00 42.14 3.50
47 48 2.682856 GGGTATTCGCACACATTGACAT 59.317 45.455 0.00 0.00 0.00 3.06
95 96 6.537301 TCGCGTTTTATTAGGAAACTGATCAT 59.463 34.615 5.77 0.00 43.88 2.45
146 147 4.679662 TCTTCGGAAACTAATCACGATCC 58.320 43.478 0.00 0.00 33.26 3.36
164 165 6.952935 ACTAATCACAATCACGTCTTCTTC 57.047 37.500 0.00 0.00 0.00 2.87
258 259 7.807907 CACTTAACAATTTACATTGACTGACCC 59.192 37.037 8.57 0.00 42.35 4.46
361 362 0.671251 ACCCCGTAAAACGTACACGA 59.329 50.000 15.51 0.00 40.58 4.35
484 2050 0.664761 CCGCATGATTAAGCCCACTG 59.335 55.000 0.00 0.00 0.00 3.66
515 2081 2.616001 GCACCCCATAAAAGGTACACGA 60.616 50.000 0.00 0.00 33.52 4.35
523 2089 7.781056 ACTATTTTACATGCACCCCATAAAAG 58.219 34.615 0.00 0.00 29.59 2.27
579 2145 5.028802 TCTCCACTTCCATCTTCATCTTCT 58.971 41.667 0.00 0.00 0.00 2.85
580 2146 5.104982 AGTCTCCACTTCCATCTTCATCTTC 60.105 44.000 0.00 0.00 0.00 2.87
581 2147 4.782156 AGTCTCCACTTCCATCTTCATCTT 59.218 41.667 0.00 0.00 0.00 2.40
583 2149 4.405358 AGAGTCTCCACTTCCATCTTCATC 59.595 45.833 0.00 0.00 30.63 2.92
584 2150 4.161942 CAGAGTCTCCACTTCCATCTTCAT 59.838 45.833 0.00 0.00 30.63 2.57
585 2151 3.513119 CAGAGTCTCCACTTCCATCTTCA 59.487 47.826 0.00 0.00 30.63 3.02
586 2152 3.678529 GCAGAGTCTCCACTTCCATCTTC 60.679 52.174 0.00 0.00 30.63 2.87
587 2153 2.235898 GCAGAGTCTCCACTTCCATCTT 59.764 50.000 0.00 0.00 30.63 2.40
588 2154 1.830477 GCAGAGTCTCCACTTCCATCT 59.170 52.381 0.00 0.00 30.63 2.90
589 2155 1.552337 TGCAGAGTCTCCACTTCCATC 59.448 52.381 0.00 0.00 30.63 3.51
590 2156 1.649321 TGCAGAGTCTCCACTTCCAT 58.351 50.000 0.00 0.00 30.63 3.41
591 2157 1.649321 ATGCAGAGTCTCCACTTCCA 58.351 50.000 0.00 0.00 30.63 3.53
592 2158 3.244044 GGATATGCAGAGTCTCCACTTCC 60.244 52.174 0.00 0.00 30.63 3.46
593 2159 3.386078 TGGATATGCAGAGTCTCCACTTC 59.614 47.826 0.00 0.00 31.19 3.01
594 2160 3.378512 TGGATATGCAGAGTCTCCACTT 58.621 45.455 0.00 0.00 31.19 3.16
595 2161 2.964464 CTGGATATGCAGAGTCTCCACT 59.036 50.000 18.72 0.00 32.71 4.00
596 2162 2.961741 TCTGGATATGCAGAGTCTCCAC 59.038 50.000 21.70 0.00 32.71 4.02
597 2163 2.961741 GTCTGGATATGCAGAGTCTCCA 59.038 50.000 25.43 1.36 34.88 3.86
598 2164 2.030363 CGTCTGGATATGCAGAGTCTCC 60.030 54.545 25.43 13.24 0.00 3.71
599 2165 2.606795 GCGTCTGGATATGCAGAGTCTC 60.607 54.545 25.43 13.58 0.00 3.36
600 2166 1.339610 GCGTCTGGATATGCAGAGTCT 59.660 52.381 25.43 0.00 0.00 3.24
601 2167 1.777101 GCGTCTGGATATGCAGAGTC 58.223 55.000 25.43 16.30 0.00 3.36
632 2198 0.999712 TGATTTGGGGGAGAAGGACC 59.000 55.000 0.00 0.00 0.00 4.46
633 2199 1.354368 TGTGATTTGGGGGAGAAGGAC 59.646 52.381 0.00 0.00 0.00 3.85
651 2217 2.202866 CGGAGCAGTAGTGGGATGT 58.797 57.895 0.00 0.00 0.00 3.06
725 2292 3.468140 GGTGGACTACGGGGAGGC 61.468 72.222 0.00 0.00 0.00 4.70
753 2320 1.601477 TAGCCGCACCGGATCGATA 60.601 57.895 9.46 4.83 44.45 2.92
916 2484 2.472909 CGGCAATTCGGAAGGAGGC 61.473 63.158 0.00 0.42 0.00 4.70
974 2548 1.446272 CGAGCCTCCTGTCGGTTTC 60.446 63.158 0.00 0.00 32.40 2.78
979 2553 3.827898 GACCCGAGCCTCCTGTCG 61.828 72.222 0.00 0.00 35.91 4.35
1171 2745 1.267261 CGGATCGAGTACCTCCATGAC 59.733 57.143 0.00 0.00 0.00 3.06
1392 2966 1.078709 ACCTCATGCGTCGTTCATTG 58.921 50.000 0.00 0.00 0.00 2.82
1419 2993 4.584029 ACTAGAATCAACGCAATTGTCG 57.416 40.909 16.98 16.98 39.54 4.35
1423 2997 5.003804 ACCAGAACTAGAATCAACGCAATT 58.996 37.500 0.00 0.00 0.00 2.32
1444 3018 1.298859 GGATCGACAGGCACAACACC 61.299 60.000 0.00 0.00 0.00 4.16
1466 3040 4.692625 CCTCCTTGTAGATTGCGGATATTG 59.307 45.833 0.00 0.00 0.00 1.90
1473 3047 1.293924 CAGCCTCCTTGTAGATTGCG 58.706 55.000 0.00 0.00 0.00 4.85
1558 3132 2.742053 CAACGGATACCACCTTGAGTTG 59.258 50.000 0.00 0.00 33.10 3.16
1825 3400 0.179156 CAGCCCATAAAAGTGCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
2265 4073 6.096846 ACTTCTTTAAATTGTTGTGGACAGCT 59.903 34.615 0.00 0.00 39.94 4.24
2415 4223 0.463620 GGCTTTGTGGCAAACTTGGA 59.536 50.000 0.00 0.00 41.37 3.53
3432 5248 2.609459 CCAGCAGGTCGACATAATGTTC 59.391 50.000 18.91 0.00 0.00 3.18
3624 5440 5.247110 ACAACACCTTGAGACTGAGATACAT 59.753 40.000 0.00 0.00 0.00 2.29
3664 5480 5.876651 TCCTGTACAGATTATGACAGCAT 57.123 39.130 24.68 0.00 36.52 3.79
3848 5672 4.228210 TGGATTTGCTCAAGGGATAAGAGT 59.772 41.667 0.00 0.00 0.00 3.24
3904 5728 1.827344 TGAAGGCAGACTCGACATCAT 59.173 47.619 0.00 0.00 0.00 2.45
4009 5834 3.139077 CAAGTAAACCGGAGAACAGCTT 58.861 45.455 9.46 0.00 0.00 3.74
4051 5877 2.662156 GCAGAGCTCGTACACAGTAAAC 59.338 50.000 8.37 0.00 0.00 2.01
4072 5898 6.932356 ATGGTATCATGAGCAGTTAACTTG 57.068 37.500 5.07 1.40 31.34 3.16
4131 5957 6.126825 ACTCAGGCAGTCAAGATTCAGATATT 60.127 38.462 0.00 0.00 0.00 1.28
4289 6278 5.436175 TCAAATAAGGATGCCGAAGATGAA 58.564 37.500 0.00 0.00 0.00 2.57
4329 6318 6.083098 ACAGCTAGTGCACTCTGATTATAG 57.917 41.667 31.46 19.66 42.74 1.31
4372 6362 5.749596 TGCATATTTTGTAGGACCGAATG 57.250 39.130 0.00 0.00 0.00 2.67
4380 6370 6.265577 GTTGTAGGCTTGCATATTTTGTAGG 58.734 40.000 0.00 0.00 0.00 3.18
4443 6433 8.598916 TCTGAATTACACTCCCACATAAAGTTA 58.401 33.333 0.00 0.00 0.00 2.24
4444 6434 7.458397 TCTGAATTACACTCCCACATAAAGTT 58.542 34.615 0.00 0.00 0.00 2.66
4445 6435 7.016153 TCTGAATTACACTCCCACATAAAGT 57.984 36.000 0.00 0.00 0.00 2.66
4446 6436 7.921786 TTCTGAATTACACTCCCACATAAAG 57.078 36.000 0.00 0.00 0.00 1.85
4447 6437 8.877864 ATTTCTGAATTACACTCCCACATAAA 57.122 30.769 0.00 0.00 0.00 1.40
4448 6438 8.106462 TGATTTCTGAATTACACTCCCACATAA 58.894 33.333 0.00 0.00 0.00 1.90
4480 6476 4.032104 GCCGACGTTAACATATTTCGAACT 59.968 41.667 6.39 0.00 0.00 3.01
4525 6529 2.002018 GAGTCCCCAAACCACCACCA 62.002 60.000 0.00 0.00 0.00 4.17
4537 6541 4.723309 TCCGTAGATAAAGTAGAGTCCCC 58.277 47.826 0.00 0.00 0.00 4.81
4541 6545 6.358991 AGCTTCTCCGTAGATAAAGTAGAGT 58.641 40.000 0.00 0.00 0.00 3.24
4597 6672 3.372676 CTGATGCCGCACTTCGCAC 62.373 63.158 0.00 0.00 42.60 5.34
4635 6710 0.592637 TGCAAGCAATTGAGTGGTCG 59.407 50.000 10.34 0.00 0.00 4.79
4646 6721 1.610038 CTGTCACAGGATTGCAAGCAA 59.390 47.619 17.68 10.19 40.47 3.91
4660 6735 1.748122 CCATGCTCCCTGCTGTCAC 60.748 63.158 0.00 0.00 43.37 3.67
4757 6835 1.906574 AGGATAACAACAGCCGGAGAA 59.093 47.619 5.05 0.00 0.00 2.87
4773 6851 3.524789 TCACCATTGTCATCTGGAAGGAT 59.475 43.478 8.55 0.00 36.35 3.24
4804 6882 3.939066 ACAAAGGGGAGTTGATCTTACG 58.061 45.455 0.00 0.00 0.00 3.18
4902 6980 1.616374 GTTTTCCGCCTTCAATTCCCA 59.384 47.619 0.00 0.00 0.00 4.37
4925 7003 9.470399 TGATCTTATAGGTTAATATCGCCACTA 57.530 33.333 0.00 0.00 0.00 2.74
4992 7077 1.338579 GCCTGGTCACTCTCAGAAAGG 60.339 57.143 0.00 0.00 33.11 3.11
5024 7109 5.645929 TGAATCCATTATGCTGTTTGTACGT 59.354 36.000 0.00 0.00 0.00 3.57
5025 7110 5.965334 GTGAATCCATTATGCTGTTTGTACG 59.035 40.000 0.00 0.00 0.00 3.67
5026 7111 6.851609 TGTGAATCCATTATGCTGTTTGTAC 58.148 36.000 0.00 0.00 0.00 2.90
5027 7112 6.404623 GCTGTGAATCCATTATGCTGTTTGTA 60.405 38.462 0.00 0.00 0.00 2.41
5028 7113 5.622914 GCTGTGAATCCATTATGCTGTTTGT 60.623 40.000 0.00 0.00 0.00 2.83
5029 7114 4.802039 GCTGTGAATCCATTATGCTGTTTG 59.198 41.667 0.00 0.00 0.00 2.93
5059 7307 3.866910 TGGAAAAACACGTACACAGAGAC 59.133 43.478 0.00 0.00 0.00 3.36
5282 7539 1.669115 CAGTGGTGCCGGAGAAGTG 60.669 63.158 5.05 0.00 0.00 3.16
5330 7587 4.081030 CTCGCGTGCTGCAAGTGG 62.081 66.667 24.64 13.99 46.97 4.00
5563 7845 1.342374 GGCCAAGGGATCCAGTTCATT 60.342 52.381 15.23 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.