Multiple sequence alignment - TraesCS6A01G366700

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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 TraesCS6A01G366700 chr6A 100.000 2652 0 0 1 2652 594318224 594320875 0.000000e+00 4898.0
1 TraesCS6A01G366700 chr6A 79.961 1557 168 69 962 2458 593992455 593990983 0.000000e+00 1014.0
2 TraesCS6A01G366700 chr6A 78.120 1170 137 54 962 2095 594254298 594253212 1.340000e-177 632.0
3 TraesCS6A01G366700 chr6A 77.597 799 99 52 1435 2190 593929568 593928807 6.830000e-111 411.0
4 TraesCS6A01G366700 chr6A 83.245 376 33 15 2088 2457 594253181 594252830 4.260000e-83 318.0
5 TraesCS6A01G366700 chr6A 79.098 488 62 23 930 1398 593930035 593929569 1.540000e-77 300.0
6 TraesCS6A01G366700 chr6A 77.751 418 56 23 1941 2339 594366495 594366894 3.440000e-54 222.0
7 TraesCS6A01G366700 chr6A 77.128 376 30 31 18 339 594255300 594254927 1.630000e-37 167.0
8 TraesCS6A01G366700 chr6A 92.308 117 8 1 2511 2626 594245310 594245194 5.870000e-37 165.0
9 TraesCS6A01G366700 chr6A 85.135 74 7 2 683 752 593930240 593930167 3.660000e-09 73.1
10 TraesCS6A01G366700 chr6D 88.363 1710 112 37 910 2564 447737608 447739285 0.000000e+00 1975.0
11 TraesCS6A01G366700 chr6D 84.151 978 86 29 1674 2624 447278099 447277164 0.000000e+00 883.0
12 TraesCS6A01G366700 chr6D 79.523 923 103 45 890 1762 447279012 447278126 1.770000e-161 579.0
13 TraesCS6A01G366700 chr6D 95.673 208 6 3 477 681 328503656 328503449 5.470000e-87 331.0
14 TraesCS6A01G366700 chr6D 94.762 210 8 2 472 678 90441599 90441808 9.160000e-85 324.0
15 TraesCS6A01G366700 chr6D 94.737 209 8 3 473 678 141388606 141388814 3.290000e-84 322.0
16 TraesCS6A01G366700 chr6D 90.303 165 9 4 772 933 447445246 447445086 2.670000e-50 209.0
17 TraesCS6A01G366700 chr6D 79.422 277 19 24 7 257 447737145 447737409 7.600000e-36 161.0
18 TraesCS6A01G366700 chr6D 89.167 120 12 1 682 801 447279151 447279033 5.910000e-32 148.0
19 TraesCS6A01G366700 chr6D 75.562 356 43 21 1045 1400 447445025 447444714 4.600000e-28 135.0
20 TraesCS6A01G366700 chr6D 91.489 47 2 2 687 732 447214105 447214060 2.200000e-06 63.9
21 TraesCS6A01G366700 chr6B 81.348 1973 182 83 680 2588 678174394 678176244 0.000000e+00 1434.0
22 TraesCS6A01G366700 chr6B 80.247 2025 203 113 683 2626 678093046 678091138 0.000000e+00 1341.0
23 TraesCS6A01G366700 chr6B 78.341 1736 189 90 815 2487 678356770 678358381 0.000000e+00 950.0
24 TraesCS6A01G366700 chr6B 77.934 1278 145 70 918 2149 677045720 677044534 0.000000e+00 671.0
25 TraesCS6A01G366700 chr6B 76.923 1313 174 70 1066 2322 678542695 678543934 6.230000e-176 627.0
26 TraesCS6A01G366700 chr6B 78.443 1053 120 60 815 1835 676866043 676865066 2.940000e-164 588.0
27 TraesCS6A01G366700 chr6B 80.185 757 104 23 890 1621 677088459 677087724 2.340000e-145 525.0
28 TraesCS6A01G366700 chr6B 86.307 482 30 14 1894 2348 676865054 676864582 2.370000e-135 492.0
29 TraesCS6A01G366700 chr6B 77.848 790 91 40 1402 2151 677336617 677335872 1.900000e-111 412.0
30 TraesCS6A01G366700 chr6B 78.819 491 71 27 918 1400 676538407 676537942 1.540000e-77 300.0
31 TraesCS6A01G366700 chr6B 83.285 347 26 11 116 435 678173999 678174340 9.290000e-75 291.0
32 TraesCS6A01G366700 chr6B 81.152 382 28 22 1844 2190 676730040 676729668 1.570000e-67 267.0
33 TraesCS6A01G366700 chr6B 83.013 312 36 9 890 1193 676730849 676730547 1.570000e-67 267.0
34 TraesCS6A01G366700 chr6B 83.704 270 28 9 1929 2191 675612847 675612587 9.490000e-60 241.0
35 TraesCS6A01G366700 chr6B 86.512 215 26 2 261 475 677046127 677045916 1.590000e-57 233.0
36 TraesCS6A01G366700 chr6B 84.874 238 25 8 2393 2624 677044534 677044302 2.050000e-56 230.0
37 TraesCS6A01G366700 chr6B 86.385 213 14 8 720 929 677129708 677129508 4.440000e-53 219.0
38 TraesCS6A01G366700 chr6B 75.816 521 62 35 682 1188 677337151 677336681 3.460000e-49 206.0
39 TraesCS6A01G366700 chr6B 83.406 229 18 8 2405 2626 676859423 676859208 7.490000e-46 195.0
40 TraesCS6A01G366700 chr6B 83.406 229 18 8 2405 2626 677079706 677079491 7.490000e-46 195.0
41 TraesCS6A01G366700 chr6B 83.628 226 17 8 2408 2626 677774639 677774427 7.490000e-46 195.0
42 TraesCS6A01G366700 chr6B 83.406 229 18 8 2405 2626 677906750 677906535 7.490000e-46 195.0
43 TraesCS6A01G366700 chr6B 85.946 185 18 5 261 441 676866358 676866178 9.690000e-45 191.0
44 TraesCS6A01G366700 chr6B 85.714 189 13 8 2453 2639 678178092 678178268 1.250000e-43 187.0
45 TraesCS6A01G366700 chr6B 77.907 258 33 12 1985 2227 676037095 676037343 3.560000e-29 139.0
46 TraesCS6A01G366700 chr6B 89.720 107 6 3 284 389 677567875 677567773 5.960000e-27 132.0
47 TraesCS6A01G366700 chr6B 78.667 225 24 11 50 260 676498753 676498539 7.710000e-26 128.0
48 TraesCS6A01G366700 chr6B 90.805 87 8 0 171 257 678354125 678354211 1.670000e-22 117.0
49 TraesCS6A01G366700 chr6B 81.935 155 10 4 680 834 677045883 677045747 6.000000e-22 115.0
50 TraesCS6A01G366700 chr6B 76.652 227 26 19 50 260 676731319 676731104 1.680000e-17 100.0
51 TraesCS6A01G366700 chr6B 76.000 225 31 13 50 260 676373010 676372795 7.820000e-16 95.3
52 TraesCS6A01G366700 chr6B 83.146 89 15 0 1480 1568 676537898 676537810 6.080000e-12 82.4
53 TraesCS6A01G366700 chr6B 86.111 72 7 3 682 752 676730944 676730875 1.020000e-09 75.0
54 TraesCS6A01G366700 chr6B 93.750 48 3 0 682 729 678356674 678356721 3.660000e-09 73.1
55 TraesCS6A01G366700 chr7A 95.305 213 7 3 472 681 535468574 535468362 4.230000e-88 335.0
56 TraesCS6A01G366700 chr3B 94.884 215 8 3 470 681 41582692 41582478 1.520000e-87 333.0
57 TraesCS6A01G366700 chr7D 95.673 208 6 3 477 681 426172192 426171985 5.470000e-87 331.0
58 TraesCS6A01G366700 chr7D 94.313 211 8 4 471 678 80321741 80321950 1.180000e-83 320.0
59 TraesCS6A01G366700 chr4D 94.470 217 8 4 469 681 48708923 48708707 5.470000e-87 331.0
60 TraesCS6A01G366700 chr5D 94.811 212 8 3 473 681 87803614 87803403 7.080000e-86 327.0


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 TraesCS6A01G366700 chr6A 594318224 594320875 2651 False 4898.000000 4898 100.000000 1 2652 1 chr6A.!!$F1 2651
1 TraesCS6A01G366700 chr6A 593990983 593992455 1472 True 1014.000000 1014 79.961000 962 2458 1 chr6A.!!$R1 1496
2 TraesCS6A01G366700 chr6A 594252830 594255300 2470 True 372.333333 632 79.497667 18 2457 3 chr6A.!!$R4 2439
3 TraesCS6A01G366700 chr6A 593928807 593930240 1433 True 261.366667 411 80.610000 683 2190 3 chr6A.!!$R3 1507
4 TraesCS6A01G366700 chr6D 447737145 447739285 2140 False 1068.000000 1975 83.892500 7 2564 2 chr6D.!!$F3 2557
5 TraesCS6A01G366700 chr6D 447277164 447279151 1987 True 536.666667 883 84.280333 682 2624 3 chr6D.!!$R3 1942
6 TraesCS6A01G366700 chr6B 678091138 678093046 1908 True 1341.000000 1341 80.247000 683 2626 1 chr6B.!!$R11 1943
7 TraesCS6A01G366700 chr6B 678173999 678178268 4269 False 637.333333 1434 83.449000 116 2639 3 chr6B.!!$F3 2523
8 TraesCS6A01G366700 chr6B 678542695 678543934 1239 False 627.000000 627 76.923000 1066 2322 1 chr6B.!!$F2 1256
9 TraesCS6A01G366700 chr6B 677087724 677088459 735 True 525.000000 525 80.185000 890 1621 1 chr6B.!!$R6 731
10 TraesCS6A01G366700 chr6B 676864582 676866358 1776 True 423.666667 588 83.565333 261 2348 3 chr6B.!!$R14 2087
11 TraesCS6A01G366700 chr6B 678354125 678358381 4256 False 380.033333 950 87.632000 171 2487 3 chr6B.!!$F4 2316
12 TraesCS6A01G366700 chr6B 677044302 677046127 1825 True 312.250000 671 82.813750 261 2624 4 chr6B.!!$R15 2363
13 TraesCS6A01G366700 chr6B 677335872 677337151 1279 True 309.000000 412 76.832000 682 2151 2 chr6B.!!$R16 1469

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
976 3341 0.238289 CTGGCTATAAATTGCGGCCG 59.762 55.0 24.05 24.05 45.06 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 4835 0.243365 TGTTGCGGCAAATCATCCAC 59.757 50.0 18.23 3.48 0.0 4.02 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
45 46 4.104143 CCATTACGGCGAGTGGTC 57.896 61.111 16.62 0.00 0.00 4.02
59 63 2.962253 GGTCGCTGATGCTACGGC 60.962 66.667 4.82 4.82 35.96 5.68
66 70 4.082192 GATGCTACGGCGTCGAAA 57.918 55.556 20.03 2.01 43.35 3.46
92 96 3.053896 GTCGGCCGGGTTTCAAGG 61.054 66.667 27.83 0.00 0.00 3.61
94 98 2.746277 CGGCCGGGTTTCAAGGAG 60.746 66.667 20.10 0.00 0.00 3.69
100 104 1.377333 GGGTTTCAAGGAGAGCGGG 60.377 63.158 0.00 0.00 0.00 6.13
159 178 0.528466 CGTCACATCCATCAGGTCCG 60.528 60.000 0.00 0.00 35.89 4.79
160 179 0.537188 GTCACATCCATCAGGTCCGT 59.463 55.000 0.00 0.00 35.89 4.69
161 180 0.536724 TCACATCCATCAGGTCCGTG 59.463 55.000 0.00 0.00 35.89 4.94
168 202 1.690633 ATCAGGTCCGTGCCATCCT 60.691 57.895 0.00 0.00 0.00 3.24
209 244 6.123045 TCGGAGATAAGTTCCCTTTTTCTT 57.877 37.500 0.00 0.00 31.89 2.52
291 350 3.854669 CAGCGAGGAATCGGGGCT 61.855 66.667 0.00 0.00 0.00 5.19
341 1933 4.717629 CGCGGTGTGCTCCTCGAA 62.718 66.667 0.00 0.00 43.27 3.71
363 1955 7.808381 TCGAAATAATATCAGGCGTCTAGAAAG 59.192 37.037 0.00 0.00 0.00 2.62
376 1968 2.043115 TCTAGAAAGGTGCTCCTCCTGA 59.957 50.000 7.99 6.53 44.35 3.86
405 1997 8.794335 ACACTTTTTCTGAAGAGAAACTTACT 57.206 30.769 9.08 0.00 45.90 2.24
475 2067 4.449068 GTGCACAGACCATCCGATTAATAG 59.551 45.833 13.17 0.00 0.00 1.73
479 2620 4.283722 ACAGACCATCCGATTAATAGTCCC 59.716 45.833 0.00 0.00 0.00 4.46
492 2633 9.480053 CGATTAATAGTCCCTCCGTTTTTATTA 57.520 33.333 0.00 0.00 0.00 0.98
496 2637 5.095145 AGTCCCTCCGTTTTTATTACTCC 57.905 43.478 0.00 0.00 0.00 3.85
498 2639 2.610833 CCCTCCGTTTTTATTACTCCGC 59.389 50.000 0.00 0.00 0.00 5.54
499 2640 3.264104 CCTCCGTTTTTATTACTCCGCA 58.736 45.455 0.00 0.00 0.00 5.69
500 2641 3.875134 CCTCCGTTTTTATTACTCCGCAT 59.125 43.478 0.00 0.00 0.00 4.73
501 2642 5.051816 CCTCCGTTTTTATTACTCCGCATA 58.948 41.667 0.00 0.00 0.00 3.14
502 2643 5.699458 CCTCCGTTTTTATTACTCCGCATAT 59.301 40.000 0.00 0.00 0.00 1.78
505 2646 8.075593 TCCGTTTTTATTACTCCGCATATTAC 57.924 34.615 0.00 0.00 0.00 1.89
506 2647 7.710044 TCCGTTTTTATTACTCCGCATATTACA 59.290 33.333 0.00 0.00 0.00 2.41
507 2648 8.007716 CCGTTTTTATTACTCCGCATATTACAG 58.992 37.037 0.00 0.00 0.00 2.74
511 2652 9.602568 TTTTATTACTCCGCATATTACAGTTGA 57.397 29.630 0.00 0.00 0.00 3.18
513 2654 4.737855 ACTCCGCATATTACAGTTGACT 57.262 40.909 0.00 0.00 0.00 3.41
515 2656 4.159693 ACTCCGCATATTACAGTTGACTGA 59.840 41.667 17.42 0.00 46.59 3.41
516 2657 5.079689 TCCGCATATTACAGTTGACTGAA 57.920 39.130 17.42 7.99 46.59 3.02
519 2660 6.257849 TCCGCATATTACAGTTGACTGAAATC 59.742 38.462 17.42 0.42 46.59 2.17
520 2661 6.037062 CCGCATATTACAGTTGACTGAAATCA 59.963 38.462 17.42 0.06 46.59 2.57
521 2662 7.413988 CCGCATATTACAGTTGACTGAAATCAA 60.414 37.037 17.42 4.37 46.59 2.57
522 2663 7.962373 CGCATATTACAGTTGACTGAAATCAAA 59.038 33.333 17.42 3.18 46.59 2.69
527 2668 8.909708 TTACAGTTGACTGAAATCAAACTTTG 57.090 30.769 17.42 0.00 46.59 2.77
528 2669 6.924111 ACAGTTGACTGAAATCAAACTTTGT 58.076 32.000 17.42 0.00 46.59 2.83
531 2672 9.352784 CAGTTGACTGAAATCAAACTTTGTAAA 57.647 29.630 5.19 0.00 46.59 2.01
592 2745 9.797642 AGCATAACAAATCTATATGATGTGGAA 57.202 29.630 9.00 0.56 43.15 3.53
603 2756 9.764363 TCTATATGATGTGGAAGTACATTCAAC 57.236 33.333 0.00 0.95 41.15 3.18
607 2760 4.804608 TGTGGAAGTACATTCAACAACG 57.195 40.909 10.88 0.00 46.75 4.10
609 2762 4.876679 TGTGGAAGTACATTCAACAACGAA 59.123 37.500 10.88 0.00 46.75 3.85
611 2764 6.077838 GTGGAAGTACATTCAACAACGAATC 58.922 40.000 0.00 0.00 41.01 2.52
614 2767 7.658167 TGGAAGTACATTCAACAACGAATCTAA 59.342 33.333 0.00 0.00 39.91 2.10
615 2768 8.665685 GGAAGTACATTCAACAACGAATCTAAT 58.334 33.333 0.00 0.00 39.91 1.73
616 2769 9.478019 GAAGTACATTCAACAACGAATCTAATG 57.522 33.333 0.00 0.00 37.88 1.90
617 2770 8.771920 AGTACATTCAACAACGAATCTAATGA 57.228 30.769 0.00 0.00 33.27 2.57
618 2771 9.383519 AGTACATTCAACAACGAATCTAATGAT 57.616 29.630 0.00 0.00 33.27 2.45
718 2875 8.954950 TGCAAGAAATTGACCAGAATTTTAAA 57.045 26.923 0.00 0.00 36.00 1.52
746 2907 4.708726 ATCAGTATTCAAACCAAGCTGC 57.291 40.909 0.00 0.00 0.00 5.25
761 2922 4.488136 TGCCATGCGCCCTACCTG 62.488 66.667 4.18 0.00 36.24 4.00
763 2924 4.181010 CCATGCGCCCTACCTGCT 62.181 66.667 4.18 0.00 0.00 4.24
764 2925 2.898840 CATGCGCCCTACCTGCTG 60.899 66.667 4.18 0.00 0.00 4.41
881 3217 7.387265 AACAATGGTTTTCCTTCCCTTAATT 57.613 32.000 0.00 0.00 41.38 1.40
883 3219 8.499288 ACAATGGTTTTCCTTCCCTTAATTAA 57.501 30.769 0.00 0.00 41.38 1.40
885 3221 9.958180 CAATGGTTTTCCTTCCCTTAATTAATT 57.042 29.630 5.89 5.89 41.38 1.40
943 3296 5.281037 CCAGAATTTACCAAACTACCCCTCT 60.281 44.000 0.00 0.00 0.00 3.69
948 3301 5.494390 TTACCAAACTACCCCTCTTTCTC 57.506 43.478 0.00 0.00 0.00 2.87
949 3302 3.599348 ACCAAACTACCCCTCTTTCTCT 58.401 45.455 0.00 0.00 0.00 3.10
954 3307 3.715287 ACTACCCCTCTTTCTCTCTTCC 58.285 50.000 0.00 0.00 0.00 3.46
955 3308 1.562783 ACCCCTCTTTCTCTCTTCCG 58.437 55.000 0.00 0.00 0.00 4.30
958 3320 1.190643 CCTCTTTCTCTCTTCCGCCT 58.809 55.000 0.00 0.00 0.00 5.52
960 3322 0.898320 TCTTTCTCTCTTCCGCCTGG 59.102 55.000 0.00 0.00 0.00 4.45
976 3341 0.238289 CTGGCTATAAATTGCGGCCG 59.762 55.000 24.05 24.05 45.06 6.13
1031 3409 0.250338 GAACCACCGGAGCTCAACTT 60.250 55.000 17.19 0.00 0.00 2.66
1037 3415 3.448686 CACCGGAGCTCAACTTACATAG 58.551 50.000 17.19 0.00 0.00 2.23
1043 3421 4.865365 GGAGCTCAACTTACATAGTCACAC 59.135 45.833 17.19 0.00 35.54 3.82
1155 3576 1.453197 CCCAACTACCAATCCGCCC 60.453 63.158 0.00 0.00 0.00 6.13
1344 3765 1.165907 CCACAAGGAACGCAAGCAGA 61.166 55.000 0.00 0.00 37.99 4.26
1693 4301 6.522054 ACTAGTACATACTGCACAAACTGTT 58.478 36.000 0.00 0.00 37.10 3.16
1773 4399 2.041265 AGGCCGGGAGATTGGAGT 59.959 61.111 2.18 0.00 0.00 3.85
1789 4415 8.262601 AGATTGGAGTTTTTAAGACCCAATTT 57.737 30.769 16.27 11.34 42.45 1.82
1836 4474 7.309499 GCTGTAGATAGAGTGGCTGTACATATT 60.309 40.741 0.00 0.00 0.00 1.28
1837 4475 8.112016 TGTAGATAGAGTGGCTGTACATATTC 57.888 38.462 0.00 0.00 0.00 1.75
1838 4476 6.597832 AGATAGAGTGGCTGTACATATTCC 57.402 41.667 0.00 0.00 0.00 3.01
1839 4477 6.318913 AGATAGAGTGGCTGTACATATTCCT 58.681 40.000 0.00 0.00 0.00 3.36
1840 4478 4.679373 AGAGTGGCTGTACATATTCCTG 57.321 45.455 0.00 0.00 0.00 3.86
1841 4479 3.134458 GAGTGGCTGTACATATTCCTGC 58.866 50.000 0.00 0.00 0.00 4.85
1842 4480 2.158755 AGTGGCTGTACATATTCCTGCC 60.159 50.000 11.94 11.94 41.86 4.85
1843 4481 1.202639 TGGCTGTACATATTCCTGCCG 60.203 52.381 13.47 0.00 43.71 5.69
1844 4482 0.868406 GCTGTACATATTCCTGCCGC 59.132 55.000 0.00 0.00 0.00 6.53
1845 4483 1.541233 GCTGTACATATTCCTGCCGCT 60.541 52.381 0.00 0.00 0.00 5.52
1846 4484 2.138320 CTGTACATATTCCTGCCGCTG 58.862 52.381 0.00 0.00 0.00 5.18
1847 4485 1.484653 TGTACATATTCCTGCCGCTGT 59.515 47.619 0.00 0.00 0.00 4.40
1848 4486 2.696187 TGTACATATTCCTGCCGCTGTA 59.304 45.455 0.00 0.00 0.00 2.74
1849 4487 2.240493 ACATATTCCTGCCGCTGTAC 57.760 50.000 0.00 0.00 0.00 2.90
1850 4488 1.484653 ACATATTCCTGCCGCTGTACA 59.515 47.619 0.00 0.00 0.00 2.90
1851 4489 2.104792 ACATATTCCTGCCGCTGTACAT 59.895 45.455 0.00 0.00 0.00 2.29
1852 4490 3.323691 ACATATTCCTGCCGCTGTACATA 59.676 43.478 0.00 0.00 0.00 2.29
1859 4497 2.031870 TGCCGCTGTACATAGAGTGAT 58.968 47.619 0.00 0.00 29.49 3.06
1861 4499 2.918549 GCCGCTGTACATAGAGTGATCG 60.919 54.545 0.00 0.00 29.49 3.69
1871 4514 2.818751 AGAGTGATCGTCTTCCTCCT 57.181 50.000 0.00 0.00 0.00 3.69
1873 4516 1.679153 GAGTGATCGTCTTCCTCCTCC 59.321 57.143 0.00 0.00 0.00 4.30
2016 4773 6.602803 ACAAATTGGAGACACATACATGCATA 59.397 34.615 0.00 0.00 42.67 3.14
2086 4893 2.729491 GCCGCAACAACTTTCCGC 60.729 61.111 0.00 0.00 0.00 5.54
2236 5083 0.613012 GGGATCAGGCCAGCAACTTT 60.613 55.000 5.01 0.00 0.00 2.66
2251 5098 1.388547 ACTTTCAGCACGGCAGAAAA 58.611 45.000 14.09 4.90 41.86 2.29
2262 5109 2.093447 ACGGCAGAAAATCTCCGATTCT 60.093 45.455 18.45 0.00 38.53 2.40
2303 5150 1.518352 ATGACGCGCGCAACTGATA 60.518 52.632 32.58 9.73 0.00 2.15
2312 5159 1.006832 CGCAACTGATAAACCGAGGG 58.993 55.000 0.00 0.00 0.00 4.30
2335 5182 5.508153 GGTTTTTCTTCTTCTTTCCCTGCTC 60.508 44.000 0.00 0.00 0.00 4.26
2372 5232 2.292267 AGTATTTTGATCAGGCCAGCG 58.708 47.619 5.01 0.00 0.00 5.18
2421 5281 6.183360 CCTCGATTCTGAAGAAATTTCTGTCC 60.183 42.308 21.15 13.45 37.65 4.02
2434 5294 2.655090 TCTGTCCAAGTTTCATGGCA 57.345 45.000 0.00 0.00 37.88 4.92
2452 5312 2.337583 GCACGCTCAACTGATGAACTA 58.662 47.619 0.00 0.00 37.67 2.24
2465 5325 9.971922 CAACTGATGAACTAAGGATTTTTCTTT 57.028 29.630 0.00 0.00 0.00 2.52
2475 5335 3.829026 AGGATTTTTCTTTGTCCTGCTCC 59.171 43.478 0.00 0.00 39.54 4.70
2477 5337 4.281941 GGATTTTTCTTTGTCCTGCTCCTT 59.718 41.667 0.00 0.00 0.00 3.36
2483 5343 9.747898 TTTTTCTTTGTCCTGCTCCTTATATTA 57.252 29.630 0.00 0.00 0.00 0.98
2488 5348 8.848474 TTTGTCCTGCTCCTTATATTATAAGC 57.152 34.615 15.26 7.99 0.00 3.09
2489 5349 7.798710 TGTCCTGCTCCTTATATTATAAGCT 57.201 36.000 15.26 0.00 0.00 3.74
2490 5350 7.615403 TGTCCTGCTCCTTATATTATAAGCTG 58.385 38.462 15.26 10.25 0.00 4.24
2627 7460 7.599998 GCACAAGAAGATGGTGTTGAAAAATAT 59.400 33.333 0.00 0.00 35.05 1.28
2635 7468 6.985653 TGGTGTTGAAAAATATTTCCTCCA 57.014 33.333 0.10 2.04 43.54 3.86
2639 7472 6.751888 GTGTTGAAAAATATTTCCTCCATCCG 59.248 38.462 0.10 0.00 43.54 4.18
2640 7473 6.661377 TGTTGAAAAATATTTCCTCCATCCGA 59.339 34.615 0.10 0.00 43.54 4.55
2641 7474 7.177568 TGTTGAAAAATATTTCCTCCATCCGAA 59.822 33.333 0.10 0.00 43.54 4.30
2642 7475 7.710676 TGAAAAATATTTCCTCCATCCGAAA 57.289 32.000 0.10 0.00 43.54 3.46
2643 7476 8.128322 TGAAAAATATTTCCTCCATCCGAAAA 57.872 30.769 0.10 0.00 43.54 2.29
2644 7477 8.757877 TGAAAAATATTTCCTCCATCCGAAAAT 58.242 29.630 0.10 0.00 43.54 1.82
2650 7483 7.660030 ATTTCCTCCATCCGAAAATATTTGT 57.340 32.000 0.39 0.00 32.08 2.83
2651 7484 6.693315 TTCCTCCATCCGAAAATATTTGTC 57.307 37.500 0.39 1.54 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.401199 TGTATGCATGTTGGCGATGTG 59.599 47.619 10.16 0.00 36.28 3.21
1 2 1.748950 TGTATGCATGTTGGCGATGT 58.251 45.000 10.16 0.00 36.28 3.06
12 13 2.598394 GGCCGCCCATGTATGCAT 60.598 61.111 3.79 3.79 35.32 3.96
13 14 4.120755 TGGCCGCCCATGTATGCA 62.121 61.111 7.03 0.00 35.79 3.96
46 47 3.323136 CGACGCCGTAGCATCAGC 61.323 66.667 0.00 0.00 39.83 4.26
48 49 0.800683 CTTTCGACGCCGTAGCATCA 60.801 55.000 0.00 0.00 39.83 3.07
59 63 1.328439 CGACCTCTGAACTTTCGACG 58.672 55.000 0.00 0.00 0.00 5.12
66 70 3.382832 CCGGCCGACCTCTGAACT 61.383 66.667 30.73 0.00 0.00 3.01
146 165 1.348008 ATGGCACGGACCTGATGGAT 61.348 55.000 0.00 0.00 37.04 3.41
161 180 1.525535 AGAGCGATGCAAGGATGGC 60.526 57.895 0.00 0.51 33.57 4.40
168 202 0.790207 GAACGTTCAGAGCGATGCAA 59.210 50.000 23.12 0.00 0.00 4.08
229 264 0.752054 TGTCAGTAAACCCGTTCCGT 59.248 50.000 0.00 0.00 0.00 4.69
236 271 2.351738 GCATGTTGCTGTCAGTAAACCC 60.352 50.000 4.81 0.00 40.96 4.11
289 348 1.274596 CTGAAATTCGGCAATGCAGC 58.725 50.000 7.79 0.00 0.00 5.25
339 1931 7.873505 ACCTTTCTAGACGCCTGATATTATTTC 59.126 37.037 0.00 0.00 0.00 2.17
340 1932 7.657761 CACCTTTCTAGACGCCTGATATTATTT 59.342 37.037 0.00 0.00 0.00 1.40
341 1933 7.155328 CACCTTTCTAGACGCCTGATATTATT 58.845 38.462 0.00 0.00 0.00 1.40
363 1955 0.615331 TGTCATTCAGGAGGAGCACC 59.385 55.000 0.00 0.00 0.00 5.01
405 1997 2.835156 TCCATGTGAACCCGACTGATTA 59.165 45.455 0.00 0.00 0.00 1.75
441 2033 2.756760 GGTCTGTGCACCAATGAATCAT 59.243 45.455 15.69 0.00 36.32 2.45
442 2034 2.161855 GGTCTGTGCACCAATGAATCA 58.838 47.619 15.69 0.00 36.32 2.57
475 2067 3.867493 CGGAGTAATAAAAACGGAGGGAC 59.133 47.826 0.00 0.00 0.00 4.46
479 2620 6.780706 ATATGCGGAGTAATAAAAACGGAG 57.219 37.500 0.00 0.00 0.00 4.63
492 2633 4.159693 TCAGTCAACTGTAATATGCGGAGT 59.840 41.667 9.82 0.00 44.12 3.85
494 2635 4.729227 TCAGTCAACTGTAATATGCGGA 57.271 40.909 9.82 0.00 44.12 5.54
496 2637 7.003939 TGATTTCAGTCAACTGTAATATGCG 57.996 36.000 13.01 0.00 41.80 4.73
501 2642 9.520204 CAAAGTTTGATTTCAGTCAACTGTAAT 57.480 29.630 10.19 12.93 43.53 1.89
502 2643 8.519526 ACAAAGTTTGATTTCAGTCAACTGTAA 58.480 29.630 22.23 7.28 44.12 2.41
505 2646 8.909708 TTACAAAGTTTGATTTCAGTCAACTG 57.090 30.769 22.23 3.69 45.08 3.16
506 2647 9.573133 CTTTACAAAGTTTGATTTCAGTCAACT 57.427 29.630 22.23 0.00 37.80 3.16
507 2648 9.353999 ACTTTACAAAGTTTGATTTCAGTCAAC 57.646 29.630 22.23 0.00 46.52 3.18
583 2736 5.049749 CGTTGTTGAATGTACTTCCACATCA 60.050 40.000 10.54 0.00 38.77 3.07
584 2737 5.178623 TCGTTGTTGAATGTACTTCCACATC 59.821 40.000 10.54 9.49 38.77 3.06
586 2739 4.443621 TCGTTGTTGAATGTACTTCCACA 58.556 39.130 0.00 1.71 37.64 4.17
587 2740 5.412526 TTCGTTGTTGAATGTACTTCCAC 57.587 39.130 0.00 0.00 32.49 4.02
589 2742 6.481954 AGATTCGTTGTTGAATGTACTTCC 57.518 37.500 0.00 0.00 38.65 3.46
590 2743 9.478019 CATTAGATTCGTTGTTGAATGTACTTC 57.522 33.333 0.00 0.00 38.65 3.01
591 2744 9.214957 TCATTAGATTCGTTGTTGAATGTACTT 57.785 29.630 0.00 0.00 38.65 2.24
592 2745 8.771920 TCATTAGATTCGTTGTTGAATGTACT 57.228 30.769 0.00 0.00 38.65 2.73
660 2813 6.019640 CCAGTGCATTACAAACTTTGACAAAG 60.020 38.462 23.41 23.41 44.10 2.77
661 2814 5.809562 CCAGTGCATTACAAACTTTGACAAA 59.190 36.000 8.55 0.00 0.00 2.83
662 2815 5.105554 ACCAGTGCATTACAAACTTTGACAA 60.106 36.000 8.55 2.77 0.00 3.18
663 2816 4.400884 ACCAGTGCATTACAAACTTTGACA 59.599 37.500 8.55 0.00 0.00 3.58
664 2817 4.932146 ACCAGTGCATTACAAACTTTGAC 58.068 39.130 8.55 0.00 0.00 3.18
665 2818 5.590530 AACCAGTGCATTACAAACTTTGA 57.409 34.783 8.55 0.00 0.00 2.69
666 2819 5.580297 ACAAACCAGTGCATTACAAACTTTG 59.420 36.000 0.00 0.00 0.00 2.77
668 2821 5.337578 ACAAACCAGTGCATTACAAACTT 57.662 34.783 0.00 0.00 0.00 2.66
669 2822 6.458232 TTACAAACCAGTGCATTACAAACT 57.542 33.333 0.00 0.00 0.00 2.66
671 2824 5.694006 GCATTACAAACCAGTGCATTACAAA 59.306 36.000 0.00 0.00 35.93 2.83
672 2825 5.221322 TGCATTACAAACCAGTGCATTACAA 60.221 36.000 0.00 0.00 40.51 2.41
673 2826 4.279420 TGCATTACAAACCAGTGCATTACA 59.721 37.500 0.00 0.00 40.51 2.41
676 2829 4.039004 TCTTGCATTACAAACCAGTGCATT 59.961 37.500 0.00 0.00 44.27 3.56
677 2830 3.573538 TCTTGCATTACAAACCAGTGCAT 59.426 39.130 0.00 0.00 44.27 3.96
678 2831 2.954989 TCTTGCATTACAAACCAGTGCA 59.045 40.909 0.00 0.00 43.33 4.57
746 2907 4.181010 AGCAGGTAGGGCGCATGG 62.181 66.667 10.83 0.00 36.08 3.66
761 2922 2.101770 GCGATTCAAGGCAGCAGC 59.898 61.111 0.00 0.00 41.10 5.25
881 3217 6.999272 TGCCTGGCCGAGTTATTATTTAATTA 59.001 34.615 17.53 0.00 0.00 1.40
883 3219 5.381757 TGCCTGGCCGAGTTATTATTTAAT 58.618 37.500 17.53 0.00 0.00 1.40
885 3221 4.425180 TGCCTGGCCGAGTTATTATTTA 57.575 40.909 17.53 0.00 0.00 1.40
887 3223 3.214328 CTTGCCTGGCCGAGTTATTATT 58.786 45.455 17.53 0.00 0.00 1.40
888 3224 2.487265 CCTTGCCTGGCCGAGTTATTAT 60.487 50.000 17.53 0.00 0.00 1.28
890 3226 0.394352 CCTTGCCTGGCCGAGTTATT 60.394 55.000 17.53 0.00 0.00 1.40
891 3227 1.224592 CCTTGCCTGGCCGAGTTAT 59.775 57.895 17.53 0.00 0.00 1.89
892 3228 1.774894 AACCTTGCCTGGCCGAGTTA 61.775 55.000 17.53 0.00 0.00 2.24
893 3229 3.133365 AACCTTGCCTGGCCGAGTT 62.133 57.895 17.53 13.33 0.00 3.01
943 3296 1.194781 AGCCAGGCGGAAGAGAGAAA 61.195 55.000 5.55 0.00 0.00 2.52
948 3301 2.910688 TTTATAGCCAGGCGGAAGAG 57.089 50.000 5.55 0.00 0.00 2.85
949 3302 3.476552 CAATTTATAGCCAGGCGGAAGA 58.523 45.455 5.55 0.00 0.00 2.87
954 3307 0.238289 CCGCAATTTATAGCCAGGCG 59.762 55.000 5.55 0.00 42.35 5.52
955 3308 0.039165 GCCGCAATTTATAGCCAGGC 60.039 55.000 1.84 1.84 36.32 4.85
958 3320 1.791103 GCGGCCGCAATTTATAGCCA 61.791 55.000 43.55 0.00 44.06 4.75
960 3322 1.081442 GGCGGCCGCAATTTATAGC 60.081 57.895 46.88 25.44 44.11 2.97
1031 3409 3.071747 TGGCTTTGGTGTGTGACTATGTA 59.928 43.478 0.00 0.00 0.00 2.29
1037 3415 1.733526 GGTGGCTTTGGTGTGTGAC 59.266 57.895 0.00 0.00 0.00 3.67
1116 3537 3.245264 GGAAAGGGAGTCAAAAGGATGGA 60.245 47.826 0.00 0.00 0.00 3.41
1267 3688 2.125147 ACATGCATGTCCGACGGG 60.125 61.111 26.61 0.00 35.87 5.28
1475 3932 3.790437 ATGGGAGCGAGCTGTGGG 61.790 66.667 0.84 0.00 0.00 4.61
1593 4053 2.757917 GGAGGCTGCGGAGAGACT 60.758 66.667 8.65 1.45 32.17 3.24
1773 4399 6.459923 CCGGAATCAAATTGGGTCTTAAAAA 58.540 36.000 0.00 0.00 0.00 1.94
1789 4415 2.214376 AATTGAACAGGCCGGAATCA 57.786 45.000 10.86 10.84 0.00 2.57
1836 4474 1.032794 CTCTATGTACAGCGGCAGGA 58.967 55.000 1.45 0.00 0.00 3.86
1837 4475 0.747255 ACTCTATGTACAGCGGCAGG 59.253 55.000 1.45 0.00 0.00 4.85
1838 4476 1.405463 TCACTCTATGTACAGCGGCAG 59.595 52.381 1.45 0.00 0.00 4.85
1839 4477 1.470051 TCACTCTATGTACAGCGGCA 58.530 50.000 1.45 0.00 0.00 5.69
1840 4478 2.667137 GATCACTCTATGTACAGCGGC 58.333 52.381 0.33 0.00 0.00 6.53
1841 4479 2.290916 ACGATCACTCTATGTACAGCGG 59.709 50.000 0.33 0.00 0.00 5.52
1842 4480 3.248841 AGACGATCACTCTATGTACAGCG 59.751 47.826 0.33 0.00 0.00 5.18
1843 4481 4.822036 AGACGATCACTCTATGTACAGC 57.178 45.455 0.33 0.00 0.00 4.40
1844 4482 5.529430 AGGAAGACGATCACTCTATGTACAG 59.471 44.000 0.33 0.00 0.00 2.74
1845 4483 5.437946 AGGAAGACGATCACTCTATGTACA 58.562 41.667 0.00 0.00 0.00 2.90
1846 4484 5.049267 GGAGGAAGACGATCACTCTATGTAC 60.049 48.000 0.00 0.00 0.00 2.90
1847 4485 5.064558 GGAGGAAGACGATCACTCTATGTA 58.935 45.833 0.00 0.00 0.00 2.29
1848 4486 3.886505 GGAGGAAGACGATCACTCTATGT 59.113 47.826 0.00 0.00 0.00 2.29
1849 4487 4.141287 AGGAGGAAGACGATCACTCTATG 58.859 47.826 0.00 0.00 0.00 2.23
1850 4488 4.394729 GAGGAGGAAGACGATCACTCTAT 58.605 47.826 0.00 0.00 0.00 1.98
1851 4489 3.433882 GGAGGAGGAAGACGATCACTCTA 60.434 52.174 0.00 0.00 0.00 2.43
1852 4490 2.650322 GAGGAGGAAGACGATCACTCT 58.350 52.381 0.00 0.00 0.00 3.24
1859 4497 2.044252 CGGGGAGGAGGAAGACGA 60.044 66.667 0.00 0.00 0.00 4.20
1861 4499 2.364448 AGCGGGGAGGAGGAAGAC 60.364 66.667 0.00 0.00 0.00 3.01
1871 4514 1.685765 ACTCTATGTGCAGCGGGGA 60.686 57.895 0.00 0.00 0.00 4.81
1873 4516 0.529337 CTCACTCTATGTGCAGCGGG 60.529 60.000 0.00 0.00 45.81 6.13
1899 4552 1.429930 TGTACAAGTGGAGCAGGGAA 58.570 50.000 0.00 0.00 0.00 3.97
2016 4773 3.033909 TCCCGTCAACAGATCAGATCAT 58.966 45.455 13.14 0.00 0.00 2.45
2058 4835 0.243365 TGTTGCGGCAAATCATCCAC 59.757 50.000 18.23 3.48 0.00 4.02
2086 4893 2.158755 ACCCACACTCCAGAAACAGAAG 60.159 50.000 0.00 0.00 0.00 2.85
2217 5063 0.613012 AAAGTTGCTGGCCTGATCCC 60.613 55.000 14.77 0.00 0.00 3.85
2236 5083 1.442769 GAGATTTTCTGCCGTGCTGA 58.557 50.000 2.24 2.24 34.87 4.26
2251 5098 4.582656 AGAAATCTCGTCAGAATCGGAGAT 59.417 41.667 0.00 0.00 45.12 2.75
2262 5109 6.280855 TGAAGTTCCATAGAAATCTCGTCA 57.719 37.500 0.00 0.00 32.58 4.35
2312 5159 5.521906 AGCAGGGAAAGAAGAAGAAAAAC 57.478 39.130 0.00 0.00 0.00 2.43
2372 5232 2.001812 TCTCTCGTGAGCTGCAAATC 57.998 50.000 9.63 0.00 40.03 2.17
2421 5281 0.592637 TGAGCGTGCCATGAAACTTG 59.407 50.000 0.00 0.00 0.00 3.16
2434 5294 3.258372 TCCTTAGTTCATCAGTTGAGCGT 59.742 43.478 0.00 0.00 40.25 5.07
2452 5312 4.281941 GGAGCAGGACAAAGAAAAATCCTT 59.718 41.667 0.00 0.00 39.66 3.36
2465 5325 7.235606 ACAGCTTATAATATAAGGAGCAGGACA 59.764 37.037 18.50 0.00 32.78 4.02
2502 5372 6.289834 TGAAAGAACAGTAAAATACCACGGA 58.710 36.000 0.00 0.00 0.00 4.69
2627 7460 7.095695 GACAAATATTTTCGGATGGAGGAAA 57.904 36.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.