Multiple sequence alignment - TraesCS7B01G449800

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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 TraesCS7B01G449800 chr7B 100.000 2590 0 0 1 2590 711757141 711754552 0.000000e+00 4783.0
1 TraesCS7B01G449800 chr7B 98.519 405 2 4 1 404 711772838 711772437 0.000000e+00 712.0
2 TraesCS7B01G449800 chr7D 88.335 1886 130 35 173 2022 617736570 617734739 0.000000e+00 2182.0
3 TraesCS7B01G449800 chr7D 95.960 198 8 0 2107 2304 56294590 56294787 3.220000e-84 322.0
4 TraesCS7B01G449800 chr7D 91.824 159 10 1 2432 2590 56295146 56295301 4.340000e-53 219.0
5 TraesCS7B01G449800 chr7D 95.495 111 4 1 2334 2443 56294775 56294885 2.650000e-40 176.0
6 TraesCS7B01G449800 chr7A 91.228 1254 64 24 804 2022 711583894 711582652 0.000000e+00 1664.0
7 TraesCS7B01G449800 chr7A 89.747 829 54 12 1 827 711584988 711584189 0.000000e+00 1031.0
8 TraesCS7B01G449800 chr7A 88.398 181 17 2 1845 2022 711580946 711580767 5.610000e-52 215.0
9 TraesCS7B01G449800 chr7A 94.231 104 6 0 2120 2223 518656422 518656525 2.670000e-35 159.0
10 TraesCS7B01G449800 chr7A 94.000 100 5 1 2008 2107 711582633 711582535 1.610000e-32 150.0
11 TraesCS7B01G449800 chr7A 95.918 49 2 0 1801 1849 711581180 711581132 2.140000e-11 80.5
12 TraesCS7B01G449800 chr6D 80.148 675 90 26 875 1536 24001457 24002100 5.050000e-127 464.0
13 TraesCS7B01G449800 chr6D 79.913 687 84 36 873 1536 29089580 29090235 3.040000e-124 455.0
14 TraesCS7B01G449800 chr6D 80.065 617 87 21 933 1536 16307313 16306720 2.380000e-115 425.0
15 TraesCS7B01G449800 chr6D 78.806 670 100 26 876 1536 16523295 16522659 1.850000e-111 412.0
16 TraesCS7B01G449800 chr6D 78.930 617 87 26 930 1536 16390157 16389574 1.880000e-101 379.0
17 TraesCS7B01G449800 chr6B 82.281 570 68 22 978 1536 59723180 59723727 1.820000e-126 462.0
18 TraesCS7B01G449800 chr6B 82.105 570 69 21 978 1536 59100549 59101096 8.450000e-125 457.0
19 TraesCS7B01G449800 chr6B 81.625 566 72 18 978 1536 58812382 58812922 8.510000e-120 440.0
20 TraesCS7B01G449800 chr6B 81.227 538 63 20 976 1506 28256647 28256141 1.440000e-107 399.0
21 TraesCS7B01G449800 chr6A 81.043 575 80 18 972 1536 33535697 33535142 5.120000e-117 431.0
22 TraesCS7B01G449800 chr6A 81.019 569 75 16 976 1536 16658710 16658167 3.080000e-114 422.0
23 TraesCS7B01G449800 chr6A 80.210 571 71 26 973 1536 16700957 16701492 8.690000e-105 390.0
24 TraesCS7B01G449800 chr6A 85.057 261 28 8 927 1177 16683323 16683582 3.310000e-64 255.0
25 TraesCS7B01G449800 chr1B 80.496 564 73 18 978 1536 587472878 587473409 5.190000e-107 398.0
26 TraesCS7B01G449800 chr1D 90.686 204 19 0 2103 2306 110733217 110733420 3.280000e-69 272.0
27 TraesCS7B01G449800 chr3D 78.507 442 69 17 3 436 21684598 21685021 1.530000e-67 267.0
28 TraesCS7B01G449800 chr2B 76.518 494 65 26 81 556 98603255 98602795 3.350000e-54 222.0
29 TraesCS7B01G449800 chr4B 83.978 181 29 0 2107 2287 37303571 37303751 9.530000e-40 174.0
30 TraesCS7B01G449800 chr4B 95.098 102 5 0 2107 2208 173365607 173365506 7.420000e-36 161.0
31 TraesCS7B01G449800 chr4A 96.226 106 2 2 2103 2208 464550521 464550624 3.430000e-39 172.0
32 TraesCS7B01G449800 chr4D 92.562 121 6 2 2100 2220 500847183 500847066 1.230000e-38 171.0
33 TraesCS7B01G449800 chr5A 81.967 183 29 3 2107 2289 656863308 656863486 4.460000e-33 152.0
34 TraesCS7B01G449800 chr2A 91.667 108 7 2 2108 2215 21142258 21142363 5.770000e-32 148.0
35 TraesCS7B01G449800 chr2A 96.429 56 2 0 2535 2590 17317959 17317904 2.740000e-15 93.5


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 TraesCS7B01G449800 chr7B 711754552 711757141 2589 True 4783.0 4783 100.000000 1 2590 1 chr7B.!!$R1 2589
1 TraesCS7B01G449800 chr7D 617734739 617736570 1831 True 2182.0 2182 88.335000 173 2022 1 chr7D.!!$R1 1849
2 TraesCS7B01G449800 chr7D 56294590 56295301 711 False 239.0 322 94.426333 2107 2590 3 chr7D.!!$F1 483
3 TraesCS7B01G449800 chr7A 711580767 711584988 4221 True 628.1 1664 91.858200 1 2107 5 chr7A.!!$R1 2106
4 TraesCS7B01G449800 chr6D 24001457 24002100 643 False 464.0 464 80.148000 875 1536 1 chr6D.!!$F1 661
5 TraesCS7B01G449800 chr6D 29089580 29090235 655 False 455.0 455 79.913000 873 1536 1 chr6D.!!$F2 663
6 TraesCS7B01G449800 chr6D 16306720 16307313 593 True 425.0 425 80.065000 933 1536 1 chr6D.!!$R1 603
7 TraesCS7B01G449800 chr6D 16522659 16523295 636 True 412.0 412 78.806000 876 1536 1 chr6D.!!$R3 660
8 TraesCS7B01G449800 chr6D 16389574 16390157 583 True 379.0 379 78.930000 930 1536 1 chr6D.!!$R2 606
9 TraesCS7B01G449800 chr6B 59723180 59723727 547 False 462.0 462 82.281000 978 1536 1 chr6B.!!$F3 558
10 TraesCS7B01G449800 chr6B 59100549 59101096 547 False 457.0 457 82.105000 978 1536 1 chr6B.!!$F2 558
11 TraesCS7B01G449800 chr6B 58812382 58812922 540 False 440.0 440 81.625000 978 1536 1 chr6B.!!$F1 558
12 TraesCS7B01G449800 chr6B 28256141 28256647 506 True 399.0 399 81.227000 976 1506 1 chr6B.!!$R1 530
13 TraesCS7B01G449800 chr6A 33535142 33535697 555 True 431.0 431 81.043000 972 1536 1 chr6A.!!$R2 564
14 TraesCS7B01G449800 chr6A 16658167 16658710 543 True 422.0 422 81.019000 976 1536 1 chr6A.!!$R1 560
15 TraesCS7B01G449800 chr6A 16700957 16701492 535 False 390.0 390 80.210000 973 1536 1 chr6A.!!$F2 563
16 TraesCS7B01G449800 chr1B 587472878 587473409 531 False 398.0 398 80.496000 978 1536 1 chr1B.!!$F1 558

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
328 330 1.019673 ATGTGTGAAGATGATGCGGC 58.98 50.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 2006 0.036105 TCTGATCCAATGCAGCGTGT 60.036 50.0 0.0 0.0 32.27 4.49 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
32 33 4.823790 TGCTTACATGCTTGCTATGATG 57.176 40.909 0.00 0.00 0.00 3.07
36 37 5.457799 GCTTACATGCTTGCTATGATGTTTG 59.542 40.000 0.00 0.00 31.56 2.93
42 43 2.512692 TGCTATGATGTTTGCAGGGT 57.487 45.000 0.00 0.00 0.00 4.34
51 52 6.019779 TGATGTTTGCAGGGTAACAAATAC 57.980 37.500 5.82 0.67 38.01 1.89
53 54 4.135306 TGTTTGCAGGGTAACAAATACGA 58.865 39.130 0.00 0.00 38.01 3.43
54 55 4.579340 TGTTTGCAGGGTAACAAATACGAA 59.421 37.500 0.00 0.00 38.01 3.85
76 77 3.636764 ACCAAGTTCAAACCAAGATCCAC 59.363 43.478 0.00 0.00 0.00 4.02
104 105 4.331108 AGTTCAAGCCTCTTCTTTGGATC 58.669 43.478 0.00 0.00 0.00 3.36
140 141 5.857471 TTTTCCTAATGCATCTGGAATGG 57.143 39.130 24.70 10.55 38.24 3.16
158 159 8.189119 TGGAATGGCAAGTTTTAGTCTTTTAT 57.811 30.769 0.00 0.00 0.00 1.40
161 162 8.422577 AATGGCAAGTTTTAGTCTTTTATCCT 57.577 30.769 0.00 0.00 0.00 3.24
162 163 7.448748 TGGCAAGTTTTAGTCTTTTATCCTC 57.551 36.000 0.00 0.00 0.00 3.71
163 164 6.433093 TGGCAAGTTTTAGTCTTTTATCCTCC 59.567 38.462 0.00 0.00 0.00 4.30
164 165 6.127703 GGCAAGTTTTAGTCTTTTATCCTCCC 60.128 42.308 0.00 0.00 0.00 4.30
165 166 6.659668 GCAAGTTTTAGTCTTTTATCCTCCCT 59.340 38.462 0.00 0.00 0.00 4.20
166 167 7.827729 GCAAGTTTTAGTCTTTTATCCTCCCTA 59.172 37.037 0.00 0.00 0.00 3.53
167 168 9.734984 CAAGTTTTAGTCTTTTATCCTCCCTAA 57.265 33.333 0.00 0.00 0.00 2.69
253 254 8.178313 AGTTTAACCCTTTAATGGTCTTTCAG 57.822 34.615 6.64 0.00 34.15 3.02
327 329 2.679336 TGAATGTGTGAAGATGATGCGG 59.321 45.455 0.00 0.00 0.00 5.69
328 330 1.019673 ATGTGTGAAGATGATGCGGC 58.980 50.000 0.00 0.00 0.00 6.53
329 331 1.026182 TGTGTGAAGATGATGCGGCC 61.026 55.000 0.00 0.00 0.00 6.13
444 446 2.702592 TGAGATGTGCATGCTGATCA 57.297 45.000 20.33 12.57 0.00 2.92
451 453 4.577834 TGTGCATGCTGATCATTTATGG 57.422 40.909 20.33 0.00 31.79 2.74
509 513 4.635833 TGCATTACACAAATCGCATGAT 57.364 36.364 0.00 0.00 35.98 2.45
512 516 5.296531 TGCATTACACAAATCGCATGATAGT 59.703 36.000 0.00 0.00 33.40 2.12
536 540 6.197842 GTCAGACAAGAAAATTTGAAGTGCAG 59.802 38.462 0.00 0.00 0.00 4.41
612 616 7.015682 TCCACCAATTAAAATGAAAACCTAGCA 59.984 33.333 0.00 0.00 0.00 3.49
641 645 4.321974 CCAAAGGAGGTTTACAGAAATGGC 60.322 45.833 0.00 0.00 0.00 4.40
642 646 2.711542 AGGAGGTTTACAGAAATGGCG 58.288 47.619 0.00 0.00 0.00 5.69
648 652 4.023193 AGGTTTACAGAAATGGCGTTTCAG 60.023 41.667 28.50 23.92 46.97 3.02
665 669 6.349426 CGTTTCAGTTCATTTCATTTGCAAG 58.651 36.000 0.00 0.00 0.00 4.01
667 671 4.946445 TCAGTTCATTTCATTTGCAAGCA 58.054 34.783 0.00 0.00 0.00 3.91
711 715 6.308766 GTGCCAAACAAGCTGTAAATGAATAG 59.691 38.462 0.00 0.00 0.00 1.73
712 716 6.015519 TGCCAAACAAGCTGTAAATGAATAGT 60.016 34.615 0.00 0.00 0.00 2.12
713 717 7.175816 TGCCAAACAAGCTGTAAATGAATAGTA 59.824 33.333 0.00 0.00 0.00 1.82
738 742 3.312155 ACCCACCCCTCTATGTTTATCCT 60.312 47.826 0.00 0.00 0.00 3.24
741 745 5.133221 CCACCCCTCTATGTTTATCCTTTG 58.867 45.833 0.00 0.00 0.00 2.77
766 770 3.507786 CGGTTCCCCAAATTTCGAATTC 58.492 45.455 0.00 0.00 0.00 2.17
772 776 3.677596 CCCCAAATTTCGAATTCCGTTTG 59.322 43.478 0.00 6.17 39.75 2.93
773 777 4.303282 CCCAAATTTCGAATTCCGTTTGT 58.697 39.130 0.00 0.00 39.75 2.83
774 778 4.747605 CCCAAATTTCGAATTCCGTTTGTT 59.252 37.500 0.00 0.00 39.75 2.83
775 779 5.235401 CCCAAATTTCGAATTCCGTTTGTTT 59.765 36.000 0.00 0.00 39.75 2.83
784 788 2.482333 CCGTTTGTTTCCCACGGCA 61.482 57.895 0.00 0.00 46.45 5.69
915 1239 1.499368 GCCCATCCAATCCACCAAAT 58.501 50.000 0.00 0.00 0.00 2.32
921 1245 3.433306 TCCAATCCACCAAATCGAAGT 57.567 42.857 0.00 0.00 0.00 3.01
991 1325 3.441290 ACGTCGCCGGAGAGAAGG 61.441 66.667 8.65 0.81 38.78 3.46
1259 1611 2.202987 GCTCGCCTCACCAGATGG 60.203 66.667 0.00 0.00 42.17 3.51
1279 1637 1.790043 GCCGATTTCGTTTTTGGTTGG 59.210 47.619 0.00 0.00 37.74 3.77
1342 1702 0.512952 AACAAGAAGACGCGCATCAC 59.487 50.000 6.14 0.00 0.00 3.06
1487 1847 0.539051 CCGAGAAGGCTGACAAGGAT 59.461 55.000 0.00 0.00 0.00 3.24
1494 1860 0.813821 GGCTGACAAGGATTCCAAGC 59.186 55.000 5.29 5.76 0.00 4.01
1506 1881 0.472471 TTCCAAGCCGACCAAGAAGT 59.528 50.000 0.00 0.00 0.00 3.01
1507 1882 0.250295 TCCAAGCCGACCAAGAAGTG 60.250 55.000 0.00 0.00 0.00 3.16
1518 1893 0.955919 CAAGAAGTGGAAGGACGCCC 60.956 60.000 0.00 0.00 0.00 6.13
1529 1904 3.948719 GACGCCCCCAAGTCCACA 61.949 66.667 0.00 0.00 0.00 4.17
1536 1911 1.133482 CCCCCAAGTCCACAAAGAAGT 60.133 52.381 0.00 0.00 0.00 3.01
1591 2002 1.743321 GCTGCCGATGAGGAGTAGCT 61.743 60.000 0.00 0.00 45.00 3.32
1595 2006 1.610363 CCGATGAGGAGTAGCTAGCA 58.390 55.000 18.83 0.00 45.00 3.49
1596 2007 1.268352 CCGATGAGGAGTAGCTAGCAC 59.732 57.143 18.83 12.89 45.00 4.40
1597 2008 1.950216 CGATGAGGAGTAGCTAGCACA 59.050 52.381 18.83 0.42 0.00 4.57
1598 2009 2.287308 CGATGAGGAGTAGCTAGCACAC 60.287 54.545 18.83 14.14 0.00 3.82
1612 2023 1.925415 GCACACGCTGCATTGGATCA 61.925 55.000 0.00 0.00 46.29 2.92
1626 2037 1.739049 GATCAGAGGGAGCCTGTCG 59.261 63.158 0.00 0.00 31.76 4.35
1655 2066 3.242944 CGAGTTGCGTCCTGTATGTAATG 59.757 47.826 0.00 0.00 34.64 1.90
1672 2083 3.641437 AATGGTTCATGGTTGTCGTTG 57.359 42.857 0.00 0.00 0.00 4.10
1673 2084 2.045561 TGGTTCATGGTTGTCGTTGT 57.954 45.000 0.00 0.00 0.00 3.32
1674 2085 1.944024 TGGTTCATGGTTGTCGTTGTC 59.056 47.619 0.00 0.00 0.00 3.18
1675 2086 1.070175 GGTTCATGGTTGTCGTTGTCG 60.070 52.381 0.00 0.00 38.55 4.35
1676 2087 1.070175 GTTCATGGTTGTCGTTGTCGG 60.070 52.381 0.00 0.00 37.69 4.79
1677 2088 0.105224 TCATGGTTGTCGTTGTCGGT 59.895 50.000 0.00 0.00 37.69 4.69
1723 2134 3.748048 TCTTGCTGAACGGAATCTGAAAG 59.252 43.478 0.00 6.47 36.01 2.62
1746 2157 3.745799 TGAACTGTTTCGCCTTCCATTA 58.254 40.909 0.00 0.00 34.04 1.90
1793 2204 0.376152 CCGCATTGTGCTCATCTCAC 59.624 55.000 0.10 0.00 42.25 3.51
1865 2276 7.014134 TGGTAAATTTGTCATGTCACTGATTGT 59.986 33.333 0.00 0.00 0.00 2.71
1872 2283 5.207768 GTCATGTCACTGATTGTTGTGTTC 58.792 41.667 0.00 0.00 35.82 3.18
1901 2312 4.038642 TGAAAGTAATTTGGGTGCTTGGTC 59.961 41.667 0.00 0.00 0.00 4.02
1946 2357 2.030946 GCAAACAGCGGATGATCTACAC 59.969 50.000 0.00 0.00 0.00 2.90
1997 2411 6.598064 CCTTATCCGGTATTGTTTCTTGTTCT 59.402 38.462 0.00 0.00 0.00 3.01
2004 2418 6.568462 CGGTATTGTTTCTTGTTCTGAGCAAT 60.568 38.462 7.40 0.00 0.00 3.56
2007 2421 5.342806 TGTTTCTTGTTCTGAGCAATACG 57.657 39.130 7.40 0.00 0.00 3.06
2184 2630 2.559440 CCAGAAGGCTAATCAGAGCAC 58.441 52.381 0.00 0.00 44.76 4.40
2192 2638 1.971505 TAATCAGAGCACCAGGGGCG 61.972 60.000 8.46 0.00 36.08 6.13
2277 2723 5.560953 GCCCTATTCTGCAAACGATCAATAC 60.561 44.000 0.00 0.00 0.00 1.89
2285 2731 8.262715 TCTGCAAACGATCAATACATAAAAGA 57.737 30.769 0.00 0.00 0.00 2.52
2302 2748 9.034800 ACATAAAAGAACAATCTCTCTCTCTCT 57.965 33.333 0.00 0.00 33.77 3.10
2303 2749 9.520204 CATAAAAGAACAATCTCTCTCTCTCTC 57.480 37.037 0.00 0.00 33.77 3.20
2304 2750 7.781324 AAAAGAACAATCTCTCTCTCTCTCT 57.219 36.000 0.00 0.00 33.77 3.10
2305 2751 7.396540 AAAGAACAATCTCTCTCTCTCTCTC 57.603 40.000 0.00 0.00 33.77 3.20
2306 2752 6.319048 AGAACAATCTCTCTCTCTCTCTCT 57.681 41.667 0.00 0.00 0.00 3.10
2307 2753 6.352516 AGAACAATCTCTCTCTCTCTCTCTC 58.647 44.000 0.00 0.00 0.00 3.20
2308 2754 5.965033 ACAATCTCTCTCTCTCTCTCTCT 57.035 43.478 0.00 0.00 0.00 3.10
2309 2755 5.923204 ACAATCTCTCTCTCTCTCTCTCTC 58.077 45.833 0.00 0.00 0.00 3.20
2310 2756 5.664908 ACAATCTCTCTCTCTCTCTCTCTCT 59.335 44.000 0.00 0.00 0.00 3.10
2311 2757 6.183360 ACAATCTCTCTCTCTCTCTCTCTCTC 60.183 46.154 0.00 0.00 0.00 3.20
2312 2758 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2313 2759 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2314 2760 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2315 2761 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2316 2762 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2317 2763 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2318 2764 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2319 2765 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2320 2766 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2321 2767 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2322 2768 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2323 2769 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2324 2770 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2325 2771 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2326 2772 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2327 2773 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2328 2774 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2329 2775 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2330 2776 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2331 2777 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2332 2778 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2333 2779 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2334 2780 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2335 2781 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2336 2782 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2439 2885 0.956633 ACAACTGCAGCACAATCAGG 59.043 50.000 15.27 0.00 32.42 3.86
2466 3555 0.179004 TGAAGTGGTGCCGTGGAATT 60.179 50.000 0.00 0.00 0.00 2.17
2468 3557 1.234615 AAGTGGTGCCGTGGAATTCG 61.235 55.000 0.00 0.00 0.00 3.34
2471 3560 1.669760 GGTGCCGTGGAATTCGTCA 60.670 57.895 0.00 0.00 0.00 4.35
2472 3561 1.231958 GGTGCCGTGGAATTCGTCAA 61.232 55.000 0.00 0.00 0.00 3.18
2528 3991 2.877786 TCAGCTTCAAACGCATCTTTGA 59.122 40.909 0.00 0.00 38.18 2.69
2569 4542 3.070018 AGCAGAAAGAACATGTCTTCCG 58.930 45.455 0.00 0.00 46.36 4.30
2578 4551 1.759445 ACATGTCTTCCGCTGCTATCT 59.241 47.619 0.00 0.00 0.00 1.98
2580 4553 0.382158 TGTCTTCCGCTGCTATCTCG 59.618 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.879777 TCATAGCAAGCATGTAAGCAAACTA 59.120 36.000 7.85 0.00 36.85 2.24
32 33 4.752661 TCGTATTTGTTACCCTGCAAAC 57.247 40.909 0.00 0.00 37.41 2.93
36 37 3.075884 TGGTTCGTATTTGTTACCCTGC 58.924 45.455 0.00 0.00 0.00 4.85
42 43 7.148120 TGGTTTGAACTTGGTTCGTATTTGTTA 60.148 33.333 6.03 0.00 44.55 2.41
51 52 4.537015 GATCTTGGTTTGAACTTGGTTCG 58.463 43.478 6.03 0.00 44.55 3.95
53 54 4.099419 GTGGATCTTGGTTTGAACTTGGTT 59.901 41.667 0.00 0.00 0.00 3.67
54 55 3.636764 GTGGATCTTGGTTTGAACTTGGT 59.363 43.478 0.00 0.00 0.00 3.67
76 77 2.883386 AGAAGAGGCTTGAACTTGCAAG 59.117 45.455 24.84 24.84 46.18 4.01
117 118 5.395546 GCCATTCCAGATGCATTAGGAAAAA 60.396 40.000 27.26 13.16 42.83 1.94
118 119 4.099881 GCCATTCCAGATGCATTAGGAAAA 59.900 41.667 27.26 13.72 42.83 2.29
119 120 3.638160 GCCATTCCAGATGCATTAGGAAA 59.362 43.478 27.26 16.31 42.83 3.13
132 133 5.712152 AAGACTAAAACTTGCCATTCCAG 57.288 39.130 0.00 0.00 0.00 3.86
140 141 6.659668 AGGGAGGATAAAAGACTAAAACTTGC 59.340 38.462 0.00 0.00 0.00 4.01
158 159 2.912956 GCATGGTATGGATTAGGGAGGA 59.087 50.000 0.00 0.00 0.00 3.71
161 162 6.718593 ATTAAGCATGGTATGGATTAGGGA 57.281 37.500 0.00 0.00 0.00 4.20
162 163 7.402054 TGTATTAAGCATGGTATGGATTAGGG 58.598 38.462 0.00 0.00 0.00 3.53
163 164 8.862325 TTGTATTAAGCATGGTATGGATTAGG 57.138 34.615 0.00 0.00 0.00 2.69
165 166 9.860650 AGTTTGTATTAAGCATGGTATGGATTA 57.139 29.630 0.00 0.00 0.00 1.75
166 167 8.766994 AGTTTGTATTAAGCATGGTATGGATT 57.233 30.769 0.00 0.00 0.00 3.01
253 254 6.148948 CAGATCGGAATAGTGACAAGATCTC 58.851 44.000 0.00 0.00 40.65 2.75
451 453 7.170658 TGTTTGGCTGCTATTTTGAATTGTAAC 59.829 33.333 0.00 0.00 0.00 2.50
509 513 7.066887 TGCACTTCAAATTTTCTTGTCTGACTA 59.933 33.333 9.51 0.09 0.00 2.59
512 516 6.127647 ACTGCACTTCAAATTTTCTTGTCTGA 60.128 34.615 0.00 0.00 0.00 3.27
531 535 1.327303 TGGTGGGATTTTGACTGCAC 58.673 50.000 0.00 0.00 0.00 4.57
536 540 5.643348 GGATTTCATTTGGTGGGATTTTGAC 59.357 40.000 0.00 0.00 0.00 3.18
612 616 1.154430 TAAACCTCCTTTGGCACCCT 58.846 50.000 0.00 0.00 0.00 4.34
641 645 5.886715 TGCAAATGAAATGAACTGAAACG 57.113 34.783 0.00 0.00 0.00 3.60
642 646 6.131389 GCTTGCAAATGAAATGAACTGAAAC 58.869 36.000 0.00 0.00 0.00 2.78
665 669 5.004156 GCACTTTCGATCTCATTTCATTTGC 59.996 40.000 0.00 0.00 0.00 3.68
667 671 5.183713 TGGCACTTTCGATCTCATTTCATTT 59.816 36.000 0.00 0.00 0.00 2.32
711 715 1.038280 CATAGAGGGGTGGGTCGTAC 58.962 60.000 0.00 0.00 0.00 3.67
712 716 0.632835 ACATAGAGGGGTGGGTCGTA 59.367 55.000 0.00 0.00 0.00 3.43
713 717 0.252558 AACATAGAGGGGTGGGTCGT 60.253 55.000 0.00 0.00 0.00 4.34
801 805 7.337184 ACGGATATTTCCTCTTTTCTTCTTTCC 59.663 37.037 0.46 0.00 40.17 3.13
806 810 5.502544 CGCACGGATATTTCCTCTTTTCTTC 60.503 44.000 0.46 0.00 40.17 2.87
870 1194 1.525306 GGCGCGGGTTTTATAGGCT 60.525 57.895 8.83 0.00 0.00 4.58
915 1239 0.866061 GATTGCGCTCGCTACTTCGA 60.866 55.000 9.73 0.00 42.51 3.71
921 1245 1.371758 GATCGGATTGCGCTCGCTA 60.372 57.895 9.73 8.35 42.51 4.26
991 1325 3.878667 CCCGGCCATCTTCCCCTC 61.879 72.222 2.24 0.00 0.00 4.30
1182 1521 1.736365 GAGGACGGGGAAGATCGACC 61.736 65.000 0.00 3.20 40.42 4.79
1259 1611 1.790043 CCAACCAAAAACGAAATCGGC 59.210 47.619 7.81 0.00 44.95 5.54
1279 1637 4.767255 CCAGGACCTGCAGACGCC 62.767 72.222 17.39 13.12 37.32 5.68
1322 1682 1.724623 GTGATGCGCGTCTTCTTGTTA 59.275 47.619 28.53 4.54 0.00 2.41
1457 1817 0.458716 CCTTCTCGGCGGTCTTCTTC 60.459 60.000 7.21 0.00 0.00 2.87
1478 1838 0.690192 TCGGCTTGGAATCCTTGTCA 59.310 50.000 0.00 0.00 0.00 3.58
1487 1847 0.472471 ACTTCTTGGTCGGCTTGGAA 59.528 50.000 0.00 0.00 0.00 3.53
1494 1860 0.685097 TCCTTCCACTTCTTGGTCGG 59.315 55.000 0.00 0.00 46.97 4.79
1506 1881 3.646715 CTTGGGGGCGTCCTTCCA 61.647 66.667 5.77 2.07 35.33 3.53
1507 1882 3.623703 GACTTGGGGGCGTCCTTCC 62.624 68.421 5.77 0.00 35.33 3.46
1513 1888 2.976494 CTTTGTGGACTTGGGGGCGT 62.976 60.000 0.00 0.00 0.00 5.68
1518 1893 2.880890 CAGACTTCTTTGTGGACTTGGG 59.119 50.000 0.00 0.00 0.00 4.12
1527 1902 1.001406 CTCCTCGGCAGACTTCTTTGT 59.999 52.381 0.00 0.00 0.00 2.83
1529 1904 1.273886 GTCTCCTCGGCAGACTTCTTT 59.726 52.381 7.74 0.00 37.82 2.52
1536 1911 2.680352 GGTGGTCTCCTCGGCAGA 60.680 66.667 0.00 0.00 0.00 4.26
1574 1985 1.610363 CTAGCTACTCCTCATCGGCA 58.390 55.000 0.00 0.00 0.00 5.69
1595 2006 0.036105 TCTGATCCAATGCAGCGTGT 60.036 50.000 0.00 0.00 32.27 4.49
1596 2007 0.656259 CTCTGATCCAATGCAGCGTG 59.344 55.000 0.00 0.00 32.27 5.34
1597 2008 0.463295 CCTCTGATCCAATGCAGCGT 60.463 55.000 0.00 0.00 32.27 5.07
1598 2009 1.164662 CCCTCTGATCCAATGCAGCG 61.165 60.000 0.00 0.00 32.27 5.18
1606 2017 0.689080 GACAGGCTCCCTCTGATCCA 60.689 60.000 0.00 0.00 36.22 3.41
1612 2023 1.534235 AACACGACAGGCTCCCTCT 60.534 57.895 0.00 0.00 0.00 3.69
1655 2066 1.070175 CGACAACGACAACCATGAACC 60.070 52.381 0.00 0.00 42.66 3.62
1723 2134 0.238553 GGAAGGCGAAACAGTTCAGC 59.761 55.000 4.77 4.77 34.56 4.26
1746 2157 7.362056 CGGATCAAATTGACATGGTAAAGACTT 60.362 37.037 0.00 0.00 0.00 3.01
1793 2204 1.609072 CATGCAGCATCAAGATCCAGG 59.391 52.381 4.38 0.00 0.00 4.45
1865 2276 1.745232 ACTTTCACTGCCGAACACAA 58.255 45.000 0.00 0.00 0.00 3.33
1872 2283 2.556622 ACCCAAATTACTTTCACTGCCG 59.443 45.455 0.00 0.00 0.00 5.69
1932 2343 3.917988 TCATCATGTGTAGATCATCCGC 58.082 45.455 0.00 0.00 0.00 5.54
1997 2411 3.269178 TGTTGATCATGCGTATTGCTCA 58.731 40.909 0.00 0.00 46.63 4.26
2082 2528 1.214589 CTGCAGACAATGGCAAGCC 59.785 57.895 8.42 3.61 39.93 4.35
2119 2565 9.582648 TCAGTAACTAAATAAAGCTCCCTTTTT 57.417 29.630 0.00 0.00 41.37 1.94
2192 2638 2.222592 CGAGTTGTGGTTGTCGGAC 58.777 57.895 0.00 0.00 0.00 4.79
2277 2723 9.520204 GAGAGAGAGAGAGATTGTTCTTTTATG 57.480 37.037 0.00 0.00 30.30 1.90
2285 2731 6.157645 AGAGAGAGAGAGAGAGAGAGATTGTT 59.842 42.308 0.00 0.00 0.00 2.83
2290 2736 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2295 2741 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2296 2742 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2297 2743 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2298 2744 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2299 2745 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2300 2746 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2301 2747 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2302 2748 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2303 2749 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2304 2750 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2305 2751 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2306 2752 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2307 2753 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2308 2754 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2309 2755 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2310 2756 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2311 2757 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2312 2758 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2313 2759 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2314 2760 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2315 2761 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2316 2762 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2317 2763 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2318 2764 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2319 2765 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2320 2766 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2321 2767 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2322 2768 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2323 2769 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
2324 2770 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
2325 2771 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
2326 2772 4.271807 AGGAGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
2327 2773 5.363868 TGTTAGGAGAGAGAGAGAGAGAGAG 59.636 48.000 0.00 0.00 0.00 3.20
2328 2774 5.277250 TGTTAGGAGAGAGAGAGAGAGAGA 58.723 45.833 0.00 0.00 0.00 3.10
2329 2775 5.614324 TGTTAGGAGAGAGAGAGAGAGAG 57.386 47.826 0.00 0.00 0.00 3.20
2330 2776 5.905331 AGATGTTAGGAGAGAGAGAGAGAGA 59.095 44.000 0.00 0.00 0.00 3.10
2331 2777 6.179906 AGATGTTAGGAGAGAGAGAGAGAG 57.820 45.833 0.00 0.00 0.00 3.20
2332 2778 5.071788 GGAGATGTTAGGAGAGAGAGAGAGA 59.928 48.000 0.00 0.00 0.00 3.10
2333 2779 5.072329 AGGAGATGTTAGGAGAGAGAGAGAG 59.928 48.000 0.00 0.00 0.00 3.20
2334 2780 4.975147 AGGAGATGTTAGGAGAGAGAGAGA 59.025 45.833 0.00 0.00 0.00 3.10
2335 2781 5.310409 AGGAGATGTTAGGAGAGAGAGAG 57.690 47.826 0.00 0.00 0.00 3.20
2336 2782 5.725551 AAGGAGATGTTAGGAGAGAGAGA 57.274 43.478 0.00 0.00 0.00 3.10
2377 2823 3.135530 AGAAGAATGAGTCATACCTGGGC 59.864 47.826 5.94 1.71 0.00 5.36
2466 3555 3.700970 TCCGGGCAGCATTGACGA 61.701 61.111 0.00 0.00 30.88 4.20
2468 3557 2.045926 AGTCCGGGCAGCATTGAC 60.046 61.111 9.71 0.00 0.00 3.18
2471 3560 4.115199 GGGAGTCCGGGCAGCATT 62.115 66.667 9.71 0.00 0.00 3.56
2489 3578 4.019860 AGCTGAACTTCTGGCAATTAGAGA 60.020 41.667 0.00 0.00 0.00 3.10
2490 3579 4.260170 AGCTGAACTTCTGGCAATTAGAG 58.740 43.478 0.00 0.00 0.00 2.43
2528 3991 1.846007 TGTTGGTTTGTGCCTCACTT 58.154 45.000 0.00 0.00 35.11 3.16


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

AutoCloner maintained by Alex Coulton.