Multiple sequence alignment - TraesCS5A01G493900

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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 TraesCS5A01G493900 chr5A 100.000 4927 0 0 1 4927 662563872 662558946 0.000000e+00 9099
1 TraesCS5A01G493900 chr5A 85.238 210 14 8 1 209 295396 295589 3.010000e-47 200
2 TraesCS5A01G493900 chr4B 90.406 4086 249 70 862 4921 608942056 608946024 0.000000e+00 5241
3 TraesCS5A01G493900 chr4D 90.299 2072 126 20 2343 4409 480872452 480874453 0.000000e+00 2643
4 TraesCS5A01G493900 chr4D 94.875 1483 47 8 875 2357 480870910 480872363 0.000000e+00 2290
5 TraesCS5A01G493900 chr4D 87.017 362 29 11 4455 4808 480874459 480874810 4.620000e-105 392
6 TraesCS5A01G493900 chr6A 99.520 833 4 0 1 833 552829679 552828847 0.000000e+00 1517
7 TraesCS5A01G493900 chr6A 99.279 832 6 0 1 832 186483108 186482277 0.000000e+00 1504
8 TraesCS5A01G493900 chr6B 98.212 839 9 1 1 833 278607745 278606907 0.000000e+00 1461
9 TraesCS5A01G493900 chr7A 98.201 834 15 0 1 834 478380793 478381626 0.000000e+00 1458
10 TraesCS5A01G493900 chr7A 86.433 457 49 7 384 834 735179293 735178844 5.730000e-134 488
11 TraesCS5A01G493900 chr6D 94.611 835 38 3 1 834 127198020 127198848 0.000000e+00 1286
12 TraesCS5A01G493900 chrUn 86.854 852 76 14 1 833 18076011 18075177 0.000000e+00 920
13 TraesCS5A01G493900 chr7B 88.621 457 38 7 384 834 744555175 744555623 1.210000e-150 544
14 TraesCS5A01G493900 chr7B 82.915 597 77 12 243 833 708504821 708505398 9.460000e-142 514
15 TraesCS5A01G493900 chr1B 82.759 580 67 14 1 564 205900715 205901277 2.060000e-133 486
16 TraesCS5A01G493900 chr5D 87.560 209 12 9 1 209 366637 366443 3.840000e-56 230
17 TraesCS5A01G493900 chr5B 85.238 210 14 8 1 209 2005156 2005349 3.010000e-47 200
18 TraesCS5A01G493900 chr3D 82.377 244 16 10 1 244 48252910 48252694 2.340000e-43 187


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 TraesCS5A01G493900 chr5A 662558946 662563872 4926 True 9099 9099 100.000000 1 4927 1 chr5A.!!$R1 4926
1 TraesCS5A01G493900 chr4B 608942056 608946024 3968 False 5241 5241 90.406000 862 4921 1 chr4B.!!$F1 4059
2 TraesCS5A01G493900 chr4D 480870910 480874810 3900 False 1775 2643 90.730333 875 4808 3 chr4D.!!$F1 3933
3 TraesCS5A01G493900 chr6A 552828847 552829679 832 True 1517 1517 99.520000 1 833 1 chr6A.!!$R2 832
4 TraesCS5A01G493900 chr6A 186482277 186483108 831 True 1504 1504 99.279000 1 832 1 chr6A.!!$R1 831
5 TraesCS5A01G493900 chr6B 278606907 278607745 838 True 1461 1461 98.212000 1 833 1 chr6B.!!$R1 832
6 TraesCS5A01G493900 chr7A 478380793 478381626 833 False 1458 1458 98.201000 1 834 1 chr7A.!!$F1 833
7 TraesCS5A01G493900 chr6D 127198020 127198848 828 False 1286 1286 94.611000 1 834 1 chr6D.!!$F1 833
8 TraesCS5A01G493900 chrUn 18075177 18076011 834 True 920 920 86.854000 1 833 1 chrUn.!!$R1 832
9 TraesCS5A01G493900 chr7B 708504821 708505398 577 False 514 514 82.915000 243 833 1 chr7B.!!$F1 590
10 TraesCS5A01G493900 chr1B 205900715 205901277 562 False 486 486 82.759000 1 564 1 chr1B.!!$F1 563

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
580 605 2.202892 GAGGCGGGTGGAATCGAC 60.203 66.667 0.00 0.00 34.07 4.20 F
1360 1391 0.478942 TGAGACCTCCTAGATCCCCG 59.521 60.000 0.00 0.00 0.00 5.73 F
1361 1392 0.896479 GAGACCTCCTAGATCCCCGC 60.896 65.000 0.00 0.00 0.00 6.13 F
1389 1420 1.072331 AGACCACATCACTCCACAACC 59.928 52.381 0.00 0.00 0.00 3.77 F
1505 1536 1.134610 GTTTGTGGGTATCGATCGGGT 60.135 52.381 16.41 7.22 0.00 5.28 F
2770 2904 2.158310 AGCTTTAAGAGGCTTTTGGGGT 60.158 45.455 0.00 0.00 34.96 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1519 0.396001 TCACCCGATCGATACCCACA 60.396 55.000 18.66 0.00 0.00 4.17 R
2670 2804 0.250081 GGCACTCCTGTAGGCATAGC 60.250 60.000 0.00 0.00 34.44 2.97 R
3321 3459 1.000060 CTGTGTGTTTTCCATGCAGGG 60.000 52.381 12.23 12.23 38.24 4.45 R
3486 3624 9.791801 TGCCAGACATTAAGATATTATAGCAAA 57.208 29.630 0.00 0.00 0.00 3.68 R
3677 3818 7.959651 CAGAACAATGATTACTACTTCAACTGC 59.040 37.037 0.00 0.00 0.00 4.40 R
4808 4978 0.102120 CCTGAGACCGAGAGCACATC 59.898 60.000 0.00 0.00 0.00 3.06 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
241 250 2.900106 GCTGCCCTCCTGGAGTGTT 61.900 63.158 21.70 0.00 35.39 3.32
580 605 2.202892 GAGGCGGGTGGAATCGAC 60.203 66.667 0.00 0.00 34.07 4.20
859 888 7.825331 TGGTCAGATCTAAGATATCTTTCGT 57.175 36.000 22.60 9.20 37.40 3.85
860 889 8.919777 TGGTCAGATCTAAGATATCTTTCGTA 57.080 34.615 22.60 4.48 37.40 3.43
895 924 3.726291 ACCCGATGAAAACCTGTTTTG 57.274 42.857 12.39 0.67 42.26 2.44
899 928 3.067461 CCGATGAAAACCTGTTTTGTCCA 59.933 43.478 12.39 5.49 42.26 4.02
955 986 4.192000 GAGCATCCCTCGTGTGTG 57.808 61.111 0.00 0.00 0.00 3.82
1210 1241 4.540735 CCACCCCGGCCACGTATC 62.541 72.222 2.24 0.00 38.78 2.24
1226 1257 2.543238 CGTATCTCCACTCTAAACGCCC 60.543 54.545 0.00 0.00 0.00 6.13
1346 1377 1.336887 TGCAACGTAAGCCTCTGAGAC 60.337 52.381 6.17 0.00 45.62 3.36
1359 1390 1.783979 TCTGAGACCTCCTAGATCCCC 59.216 57.143 0.00 0.00 0.00 4.81
1360 1391 0.478942 TGAGACCTCCTAGATCCCCG 59.521 60.000 0.00 0.00 0.00 5.73
1361 1392 0.896479 GAGACCTCCTAGATCCCCGC 60.896 65.000 0.00 0.00 0.00 6.13
1362 1393 1.152525 GACCTCCTAGATCCCCGCA 60.153 63.158 0.00 0.00 0.00 5.69
1363 1394 1.152440 ACCTCCTAGATCCCCGCAG 60.152 63.158 0.00 0.00 0.00 5.18
1364 1395 1.152440 CCTCCTAGATCCCCGCAGT 60.152 63.158 0.00 0.00 0.00 4.40
1365 1396 1.182385 CCTCCTAGATCCCCGCAGTC 61.182 65.000 0.00 0.00 0.00 3.51
1376 1407 4.662961 CGCAGTCCGCAGACCACA 62.663 66.667 0.00 0.00 44.72 4.17
1389 1420 1.072331 AGACCACATCACTCCACAACC 59.928 52.381 0.00 0.00 0.00 3.77
1483 1514 6.203338 ACAGAATATTTTGCTTTGTGCCTTTG 59.797 34.615 5.92 0.00 42.00 2.77
1484 1515 6.203338 CAGAATATTTTGCTTTGTGCCTTTGT 59.797 34.615 0.00 0.00 42.00 2.83
1485 1516 5.927954 ATATTTTGCTTTGTGCCTTTGTG 57.072 34.783 0.00 0.00 42.00 3.33
1486 1517 2.758736 TTTGCTTTGTGCCTTTGTGT 57.241 40.000 0.00 0.00 42.00 3.72
1487 1518 2.758736 TTGCTTTGTGCCTTTGTGTT 57.241 40.000 0.00 0.00 42.00 3.32
1488 1519 2.758736 TGCTTTGTGCCTTTGTGTTT 57.241 40.000 0.00 0.00 42.00 2.83
1505 1536 1.134610 GTTTGTGGGTATCGATCGGGT 60.135 52.381 16.41 7.22 0.00 5.28
1573 1604 2.357517 CACGAGGGAGGTGTGTGC 60.358 66.667 0.00 0.00 0.00 4.57
1685 1716 2.367894 GCCTTAGGCTATAAAGGACGGT 59.632 50.000 17.16 0.00 46.69 4.83
1740 1771 3.674997 ACGCTTCATGAGGTATTTGTGT 58.325 40.909 6.70 0.00 0.00 3.72
1753 1784 2.585170 TTTGTGTGTCGCGTGTTGGC 62.585 55.000 5.77 0.00 0.00 4.52
1788 1819 4.453136 GCAAATTGTTGACATTTCCTGCAT 59.547 37.500 0.00 0.00 36.83 3.96
1796 1827 5.581126 TGACATTTCCTGCATTTGATACC 57.419 39.130 0.00 0.00 0.00 2.73
1806 1837 2.358898 GCATTTGATACCGGAAGCACAT 59.641 45.455 9.46 0.00 0.00 3.21
1807 1838 3.793129 GCATTTGATACCGGAAGCACATG 60.793 47.826 9.46 12.11 0.00 3.21
1924 1955 3.169355 ACCTTGTTGCTTTGCTGAAAG 57.831 42.857 0.00 0.00 41.49 2.62
1977 2008 4.906618 ACATAACTGTTAGGGTGTTCTGG 58.093 43.478 15.60 0.00 28.70 3.86
1990 2021 4.764823 GGGTGTTCTGGAATGTTTACATGA 59.235 41.667 0.00 0.00 36.56 3.07
1998 2029 7.999679 TCTGGAATGTTTACATGATGGAATTC 58.000 34.615 0.00 0.00 36.56 2.17
2003 2034 6.809630 TGTTTACATGATGGAATTCGTTCA 57.190 33.333 0.00 10.33 0.00 3.18
2078 2109 4.041567 TCAGACTTTGCTAGGACATTTGGA 59.958 41.667 0.00 0.00 0.00 3.53
2093 2124 7.661027 AGGACATTTGGATGGTAATTTTGTTTG 59.339 33.333 0.00 0.00 37.60 2.93
2154 2185 4.519540 AACCTCCATTTTCATTGGAACG 57.480 40.909 0.00 0.00 42.56 3.95
2158 2189 4.261994 CCTCCATTTTCATTGGAACGTGTT 60.262 41.667 0.00 0.00 42.56 3.32
2159 2190 4.615949 TCCATTTTCATTGGAACGTGTTG 58.384 39.130 0.00 0.00 40.29 3.33
2241 2272 7.106890 AGAGGTTTCTTCCTTGCTACTTTATC 58.893 38.462 0.00 0.00 38.02 1.75
2423 2557 2.654863 ACTTCCCCAGTTTTGTGACAG 58.345 47.619 0.00 0.00 27.32 3.51
2482 2616 4.264460 ACTCAGACTCAGTGGAATTGTC 57.736 45.455 0.00 0.00 0.00 3.18
2537 2671 7.874528 CCTTTTCTGCAGGAGTTAAATCAAAAT 59.125 33.333 15.13 0.00 32.41 1.82
2572 2706 2.879103 TGGAAGGTCCAAATGGAGAC 57.121 50.000 1.47 0.00 45.00 3.36
2623 2757 7.982252 ACATCCATCTGTAAGTGGATAATGAT 58.018 34.615 6.58 0.00 46.19 2.45
2722 2856 8.398665 GGTTATTTTGCTTCTATGTACAAGAGG 58.601 37.037 0.00 6.27 0.00 3.69
2770 2904 2.158310 AGCTTTAAGAGGCTTTTGGGGT 60.158 45.455 0.00 0.00 34.96 4.95
2775 2909 2.808906 AGAGGCTTTTGGGGTCATAC 57.191 50.000 0.00 0.00 0.00 2.39
2814 2948 8.738645 AGAATAAAGGTGAGCTTTTATGTAGG 57.261 34.615 15.26 0.00 37.09 3.18
2824 2958 6.025749 AGCTTTTATGTAGGTTTTGCTTCC 57.974 37.500 0.00 0.00 0.00 3.46
2873 3007 5.559148 TTGCCCATGTAATTTTGAACCTT 57.441 34.783 0.00 0.00 0.00 3.50
2890 3024 6.577103 TGAACCTTTGCAATTTGATAACACA 58.423 32.000 0.00 0.00 0.00 3.72
2949 3083 2.751166 AAGTCACTGCTCTATGCGTT 57.249 45.000 0.00 0.00 46.63 4.84
3072 3206 4.700213 ACAATTTAGAGTAAATGGCACGCT 59.300 37.500 0.00 0.00 38.32 5.07
3073 3207 5.183140 ACAATTTAGAGTAAATGGCACGCTT 59.817 36.000 0.00 0.00 38.32 4.68
3074 3208 4.678509 TTTAGAGTAAATGGCACGCTTG 57.321 40.909 0.00 0.00 0.00 4.01
3075 3209 2.185004 AGAGTAAATGGCACGCTTGT 57.815 45.000 0.00 0.00 0.00 3.16
3076 3210 3.328382 AGAGTAAATGGCACGCTTGTA 57.672 42.857 0.00 0.00 0.00 2.41
3077 3211 3.262420 AGAGTAAATGGCACGCTTGTAG 58.738 45.455 0.00 0.00 0.00 2.74
3078 3212 3.056107 AGAGTAAATGGCACGCTTGTAGA 60.056 43.478 0.00 0.00 0.00 2.59
3079 3213 3.262420 AGTAAATGGCACGCTTGTAGAG 58.738 45.455 0.00 0.00 0.00 2.43
3164 3298 7.550906 AGTTTTCTTCTTAAGCTACATAGGCTG 59.449 37.037 0.00 0.00 40.19 4.85
3217 3351 6.404293 GGCGTGTCATCAATAAGGTAAACAAT 60.404 38.462 0.00 0.00 0.00 2.71
3218 3352 7.201661 GGCGTGTCATCAATAAGGTAAACAATA 60.202 37.037 0.00 0.00 0.00 1.90
3425 3563 5.193679 GTTTGAACATATAGGCCAACCTCT 58.806 41.667 5.01 0.00 46.34 3.69
3429 3567 6.964464 TGAACATATAGGCCAACCTCTTAAA 58.036 36.000 5.01 0.00 46.34 1.52
3434 3572 8.499406 ACATATAGGCCAACCTCTTAAAACATA 58.501 33.333 5.01 0.00 46.34 2.29
3486 3624 9.787435 TTTGTTACCATTCTTCATTAGTACTGT 57.213 29.630 5.39 0.00 0.00 3.55
3677 3818 7.849515 GGTTAGTTTTCAAAACACTAGTTCGAG 59.150 37.037 15.41 0.00 36.84 4.04
3750 3895 5.043248 ACAGCAAGCACAGTTTAATTCAAC 58.957 37.500 0.00 0.00 0.00 3.18
3807 3952 3.069289 TGCTGTTGCAGAGTACAATCAG 58.931 45.455 0.00 0.00 45.31 2.90
3905 4050 1.831580 AATTCTCAGTTCTGCCTGGC 58.168 50.000 12.87 12.87 33.14 4.85
3950 4095 1.265365 GCTGTGCTGTTTCTTCCTGTC 59.735 52.381 0.00 0.00 0.00 3.51
3956 4101 2.416893 GCTGTTTCTTCCTGTCGGATTC 59.583 50.000 0.00 0.00 39.58 2.52
3974 4119 1.874019 CCGATGGACAGAAGACGCG 60.874 63.158 3.53 3.53 0.00 6.01
3979 4124 0.317160 TGGACAGAAGACGCGTGATT 59.683 50.000 20.70 11.94 0.00 2.57
3985 4130 1.000955 AGAAGACGCGTGATTCTTGGT 59.999 47.619 20.70 1.86 32.04 3.67
3986 4131 1.126846 GAAGACGCGTGATTCTTGGTG 59.873 52.381 20.70 0.00 32.04 4.17
3987 4132 0.033504 AGACGCGTGATTCTTGGTGT 59.966 50.000 20.70 0.00 0.00 4.16
3990 4135 0.439985 CGCGTGATTCTTGGTGTGAG 59.560 55.000 0.00 0.00 0.00 3.51
3995 4140 2.030805 GTGATTCTTGGTGTGAGTTGCC 60.031 50.000 0.00 0.00 0.00 4.52
4006 4151 0.179020 TGAGTTGCCCTGTTCACCTG 60.179 55.000 0.00 0.00 0.00 4.00
4015 4160 2.558359 CCCTGTTCACCTGGTCAATTTC 59.442 50.000 0.00 0.00 0.00 2.17
4021 4166 2.622942 TCACCTGGTCAATTTCTTGTGC 59.377 45.455 0.00 0.00 33.87 4.57
4052 4197 2.030540 CGACGTTCTTCCTCCTGTTACA 60.031 50.000 0.00 0.00 0.00 2.41
4069 4214 6.263516 TGTTACACTAGCTTAAGATGACGT 57.736 37.500 6.67 1.45 0.00 4.34
4094 4239 1.131638 TCAGGTTGCTCCACTCACTT 58.868 50.000 1.79 0.00 39.02 3.16
4095 4240 1.202687 TCAGGTTGCTCCACTCACTTG 60.203 52.381 1.79 0.00 39.02 3.16
4122 4267 3.819337 TCTGGTCTGATATGGTAGTACGC 59.181 47.826 0.00 0.00 0.00 4.42
4125 4270 3.552541 GTCTGATATGGTAGTACGCACG 58.447 50.000 0.00 0.00 0.00 5.34
4141 4286 3.310227 ACGCACGTGAAACAAATTACTGA 59.690 39.130 22.23 0.00 35.74 3.41
4172 4317 1.676006 CCACCCGCCATGTAATTTCTC 59.324 52.381 0.00 0.00 0.00 2.87
4248 4406 4.641645 CACAGCACAGGGGCCGAA 62.642 66.667 0.00 0.00 0.00 4.30
4249 4407 4.643387 ACAGCACAGGGGCCGAAC 62.643 66.667 0.00 0.00 0.00 3.95
4250 4408 4.335647 CAGCACAGGGGCCGAACT 62.336 66.667 0.00 0.00 0.00 3.01
4251 4409 4.335647 AGCACAGGGGCCGAACTG 62.336 66.667 16.42 16.42 40.48 3.16
4253 4411 3.953775 CACAGGGGCCGAACTGGT 61.954 66.667 20.46 7.50 41.21 4.00
4271 4429 7.448748 AACTGGTATGAGTGTAAATTTCACC 57.551 36.000 13.64 8.53 36.58 4.02
4324 4482 3.303229 GCAATAATACGGTTGCTTGTTGC 59.697 43.478 12.63 12.63 45.41 4.17
4361 4519 1.277273 CCTGCAGATCCAGTGTCAAGA 59.723 52.381 17.39 0.00 0.00 3.02
4374 4532 2.032550 GTGTCAAGATGATGCATTCCCG 59.967 50.000 0.00 0.00 0.00 5.14
4377 4535 1.605710 CAAGATGATGCATTCCCGACC 59.394 52.381 0.00 0.00 0.00 4.79
4383 4541 0.107017 ATGCATTCCCGACCTCCAAG 60.107 55.000 0.00 0.00 0.00 3.61
4384 4542 1.452108 GCATTCCCGACCTCCAAGG 60.452 63.158 0.00 0.00 42.49 3.61
4434 4595 1.295357 TACCACATTGCGCGGAACAG 61.295 55.000 17.40 14.19 0.00 3.16
4451 4612 4.260784 GGAACAGTGTCACACAAATCAGAC 60.261 45.833 11.40 0.00 36.74 3.51
4474 4635 1.177401 CTTTTACTCTGCCCCCTTGC 58.823 55.000 0.00 0.00 0.00 4.01
4478 4639 0.840288 TACTCTGCCCCCTTGCTGAA 60.840 55.000 0.00 0.00 38.50 3.02
4491 4652 3.820467 CCTTGCTGAATGTACTCCACAAA 59.180 43.478 0.00 0.00 41.55 2.83
4526 4687 8.567285 AATATTCTAGTGGTTCTTTTGGAGTG 57.433 34.615 0.00 0.00 0.00 3.51
4527 4688 3.740115 TCTAGTGGTTCTTTTGGAGTGC 58.260 45.455 0.00 0.00 0.00 4.40
4572 4733 1.903877 ATCTGTGAACCTGGGCCGAG 61.904 60.000 7.99 7.99 0.00 4.63
4592 4753 1.334149 GCGGAGTCTTTGTTGTGAAGC 60.334 52.381 0.00 0.00 0.00 3.86
4598 4759 3.251004 AGTCTTTGTTGTGAAGCGATTCC 59.749 43.478 11.45 2.97 0.00 3.01
4599 4760 2.223144 TCTTTGTTGTGAAGCGATTCCG 59.777 45.455 11.45 0.00 39.16 4.30
4600 4761 0.871722 TTGTTGTGAAGCGATTCCGG 59.128 50.000 11.45 0.00 36.06 5.14
4601 4762 0.034198 TGTTGTGAAGCGATTCCGGA 59.966 50.000 11.45 0.00 36.06 5.14
4602 4763 0.721718 GTTGTGAAGCGATTCCGGAG 59.278 55.000 11.45 0.00 36.06 4.63
4612 4773 1.339610 CGATTCCGGAGCAGAATCTCT 59.660 52.381 3.34 0.00 33.70 3.10
4618 4779 2.266554 CGGAGCAGAATCTCTTGTGTC 58.733 52.381 0.00 0.00 33.70 3.67
4627 4788 4.590647 AGAATCTCTTGTGTCTGTTCCTCA 59.409 41.667 0.00 0.00 0.00 3.86
4653 4820 1.935933 ACGCAAGGAATATCGTGACC 58.064 50.000 0.00 0.00 46.39 4.02
4682 4849 3.645212 TGGAAATCCAACTGCCAATTGAA 59.355 39.130 7.12 0.00 44.35 2.69
4694 4861 6.877236 ACTGCCAATTGAAAATAATGGGTAG 58.123 36.000 7.12 8.03 44.72 3.18
4695 4862 6.440328 ACTGCCAATTGAAAATAATGGGTAGT 59.560 34.615 7.12 9.10 46.18 2.73
4697 4864 8.006298 TGCCAATTGAAAATAATGGGTAGTAG 57.994 34.615 7.12 0.00 34.23 2.57
4698 4865 7.617723 TGCCAATTGAAAATAATGGGTAGTAGT 59.382 33.333 7.12 0.00 34.23 2.73
4699 4866 7.920682 GCCAATTGAAAATAATGGGTAGTAGTG 59.079 37.037 7.12 0.00 34.23 2.74
4700 4867 9.184523 CCAATTGAAAATAATGGGTAGTAGTGA 57.815 33.333 7.12 0.00 0.00 3.41
4734 4904 3.466791 CTAGCGTGCCCCCTGATGG 62.467 68.421 0.00 0.00 0.00 3.51
4770 4940 1.852633 ATGCTCCTTTAACCTTGGGC 58.147 50.000 0.00 0.00 0.00 5.36
4778 4948 3.768757 CCTTTAACCTTGGGCATGATGAA 59.231 43.478 0.00 0.00 0.00 2.57
4785 4955 3.067742 CCTTGGGCATGATGAATTGACTC 59.932 47.826 0.00 0.00 0.00 3.36
4786 4956 2.658285 TGGGCATGATGAATTGACTCC 58.342 47.619 0.00 0.00 0.00 3.85
4787 4957 2.242965 TGGGCATGATGAATTGACTCCT 59.757 45.455 0.00 0.00 0.00 3.69
4792 4962 6.041296 GGGCATGATGAATTGACTCCTTTATT 59.959 38.462 0.00 0.00 0.00 1.40
4808 4978 5.098893 CCTTTATTCTCGTCACTGTCTGAG 58.901 45.833 0.00 0.00 0.00 3.35
4811 4981 3.839051 TTCTCGTCACTGTCTGAGATG 57.161 47.619 4.57 0.00 37.33 2.90
4846 5016 0.962356 GTGGGTTGCTGGACCATCAG 60.962 60.000 0.00 0.00 41.65 2.90
4855 5025 0.533531 TGGACCATCAGCATCGCATC 60.534 55.000 0.00 0.00 0.00 3.91
4858 5028 1.228033 CCATCAGCATCGCATCCCA 60.228 57.895 0.00 0.00 0.00 4.37
4859 5029 0.608308 CCATCAGCATCGCATCCCAT 60.608 55.000 0.00 0.00 0.00 4.00
4860 5030 0.521735 CATCAGCATCGCATCCCATG 59.478 55.000 0.00 0.00 0.00 3.66
4861 5031 0.399075 ATCAGCATCGCATCCCATGA 59.601 50.000 0.00 0.00 0.00 3.07
4862 5032 0.399075 TCAGCATCGCATCCCATGAT 59.601 50.000 0.00 0.00 0.00 2.45
4904 5074 4.373116 GTGGGCGACTCGAGGCAA 62.373 66.667 20.47 1.75 35.71 4.52
4905 5075 3.390521 TGGGCGACTCGAGGCAAT 61.391 61.111 20.47 0.00 35.71 3.56
4907 5077 2.174319 GGGCGACTCGAGGCAATTC 61.174 63.158 20.47 4.40 35.71 2.17
4912 5082 1.363744 GACTCGAGGCAATTCTGGTG 58.636 55.000 15.11 0.00 0.00 4.17
4915 5085 1.466167 CTCGAGGCAATTCTGGTGTTG 59.534 52.381 3.91 0.00 0.00 3.33
4921 5091 5.294734 AGGCAATTCTGGTGTTGATTTTT 57.705 34.783 0.00 0.00 0.00 1.94
4922 5092 5.058490 AGGCAATTCTGGTGTTGATTTTTG 58.942 37.500 0.00 0.00 0.00 2.44
4923 5093 5.055812 GGCAATTCTGGTGTTGATTTTTGA 58.944 37.500 0.00 0.00 0.00 2.69
4924 5094 5.526846 GGCAATTCTGGTGTTGATTTTTGAA 59.473 36.000 0.00 0.00 0.00 2.69
4925 5095 6.293027 GGCAATTCTGGTGTTGATTTTTGAAG 60.293 38.462 0.00 0.00 0.00 3.02
4926 5096 6.479660 GCAATTCTGGTGTTGATTTTTGAAGA 59.520 34.615 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
834 863 8.415950 ACGAAAGATATCTTAGATCTGACCAT 57.584 34.615 18.23 0.00 33.85 3.55
835 864 7.825331 ACGAAAGATATCTTAGATCTGACCA 57.175 36.000 18.23 0.00 33.85 4.02
836 865 9.997482 GATACGAAAGATATCTTAGATCTGACC 57.003 37.037 18.23 0.33 33.85 4.02
873 902 4.645588 ACAAAACAGGTTTTCATCGGGTTA 59.354 37.500 7.15 0.00 40.45 2.85
879 908 6.208599 TCCTATGGACAAAACAGGTTTTCATC 59.791 38.462 7.15 8.10 40.45 2.92
895 924 2.954318 TGTAGTACGCCTTCCTATGGAC 59.046 50.000 0.00 0.00 0.00 4.02
899 928 5.564259 CGCTTATTGTAGTACGCCTTCCTAT 60.564 44.000 0.00 0.00 0.00 2.57
1195 1226 3.152400 GAGATACGTGGCCGGGGT 61.152 66.667 2.18 0.00 38.78 4.95
1196 1227 3.925090 GGAGATACGTGGCCGGGG 61.925 72.222 2.18 0.00 38.78 5.73
1197 1228 3.151710 TGGAGATACGTGGCCGGG 61.152 66.667 2.18 0.00 38.78 5.73
1198 1229 2.106332 GTGGAGATACGTGGCCGG 59.894 66.667 0.00 0.00 38.78 6.13
1210 1241 0.175989 GGAGGGCGTTTAGAGTGGAG 59.824 60.000 0.00 0.00 0.00 3.86
1346 1377 1.152440 ACTGCGGGGATCTAGGAGG 60.152 63.158 0.00 0.00 0.00 4.30
1360 1391 2.046892 ATGTGGTCTGCGGACTGC 60.047 61.111 24.48 17.12 46.70 4.40
1361 1392 1.016130 GTGATGTGGTCTGCGGACTG 61.016 60.000 24.48 0.00 41.82 3.51
1362 1393 1.188219 AGTGATGTGGTCTGCGGACT 61.188 55.000 24.48 5.18 41.82 3.85
1363 1394 0.737715 GAGTGATGTGGTCTGCGGAC 60.738 60.000 17.83 17.83 41.43 4.79
1364 1395 1.591703 GAGTGATGTGGTCTGCGGA 59.408 57.895 0.00 0.00 0.00 5.54
1365 1396 1.448540 GGAGTGATGTGGTCTGCGG 60.449 63.158 0.00 0.00 0.00 5.69
1376 1407 1.237285 GCTTGCGGTTGTGGAGTGAT 61.237 55.000 0.00 0.00 0.00 3.06
1483 1514 1.931172 CCGATCGATACCCACAAACAC 59.069 52.381 18.66 0.00 0.00 3.32
1484 1515 1.134640 CCCGATCGATACCCACAAACA 60.135 52.381 18.66 0.00 0.00 2.83
1485 1516 1.134610 ACCCGATCGATACCCACAAAC 60.135 52.381 18.66 0.00 0.00 2.93
1486 1517 1.134640 CACCCGATCGATACCCACAAA 60.135 52.381 18.66 0.00 0.00 2.83
1487 1518 0.462375 CACCCGATCGATACCCACAA 59.538 55.000 18.66 0.00 0.00 3.33
1488 1519 0.396001 TCACCCGATCGATACCCACA 60.396 55.000 18.66 0.00 0.00 4.17
1573 1604 3.248363 TGAATTTGATATGAAGCGAGGCG 59.752 43.478 0.00 0.00 0.00 5.52
1578 1609 7.325338 GGTGATGATTGAATTTGATATGAAGCG 59.675 37.037 0.00 0.00 0.00 4.68
1640 1671 2.487934 CACAAGAGGACCAGTGTTCAG 58.512 52.381 0.00 0.00 0.00 3.02
1685 1716 1.816679 GGCGATCACAGCATCAGCA 60.817 57.895 0.00 0.00 45.49 4.41
1753 1784 5.060816 GTCAACAATTTGCACCAATATCGTG 59.939 40.000 0.00 0.00 32.17 4.35
1788 1819 2.746904 CACATGTGCTTCCGGTATCAAA 59.253 45.455 13.94 0.00 0.00 2.69
1806 1837 0.822944 CCATTCACCACCTGCACACA 60.823 55.000 0.00 0.00 0.00 3.72
1807 1838 1.959085 CCATTCACCACCTGCACAC 59.041 57.895 0.00 0.00 0.00 3.82
1859 1890 1.006805 GTGATCAGGCCCTCGATCG 60.007 63.158 9.36 9.36 40.80 3.69
1977 2008 7.967854 TGAACGAATTCCATCATGTAAACATTC 59.032 33.333 0.00 0.00 31.99 2.67
1990 2021 4.572389 GCATCACTACTGAACGAATTCCAT 59.428 41.667 0.00 0.00 33.49 3.41
1998 2029 3.494626 ACAAAGTGCATCACTACTGAACG 59.505 43.478 12.87 0.00 44.62 3.95
2003 2034 6.699575 AGAAAAACAAAGTGCATCACTACT 57.300 33.333 0.00 0.00 44.62 2.57
2154 2185 6.200097 CCTGGTTTAACAAGCAATAACAACAC 59.800 38.462 0.00 0.00 39.90 3.32
2158 2189 5.594725 TGACCTGGTTTAACAAGCAATAACA 59.405 36.000 0.00 0.00 39.90 2.41
2159 2190 6.079424 TGACCTGGTTTAACAAGCAATAAC 57.921 37.500 0.00 0.00 39.90 1.89
2241 2272 9.887629 AAGAATCAACATAGATGCTATATGAGG 57.112 33.333 9.43 3.21 32.56 3.86
2268 2299 5.345202 CGTGTACTTTACTTGCTAACAGAGG 59.655 44.000 0.00 0.00 0.00 3.69
2423 2557 6.325919 TCATGTTGGTCTTGGTTTCATAAC 57.674 37.500 0.00 0.00 0.00 1.89
2482 2616 1.277273 TGAGTCTGAGATGTTGGGCAG 59.723 52.381 0.00 0.00 0.00 4.85
2537 2671 4.209538 CCTTCCATCATGCCAATGTCTAA 58.790 43.478 0.00 0.00 35.15 2.10
2651 2785 8.510505 GGCATAGCAATTTTTAAATTTCCAACA 58.489 29.630 0.00 0.00 36.52 3.33
2652 2786 8.729756 AGGCATAGCAATTTTTAAATTTCCAAC 58.270 29.630 0.00 0.00 36.52 3.77
2659 2793 8.305046 TCCTGTAGGCATAGCAATTTTTAAAT 57.695 30.769 0.00 0.00 34.44 1.40
2662 2796 6.318648 CACTCCTGTAGGCATAGCAATTTTTA 59.681 38.462 0.00 0.00 34.44 1.52
2670 2804 0.250081 GGCACTCCTGTAGGCATAGC 60.250 60.000 0.00 0.00 34.44 2.97
2722 2856 6.586082 CCAGAACATAACATAAGTTGCCAAAC 59.414 38.462 0.00 0.00 38.69 2.93
2775 2909 9.534565 TCACCTTTATTCTCAAATCTCGATTAG 57.465 33.333 0.00 0.00 0.00 1.73
2814 2948 2.860136 GCAACTCACTTGGAAGCAAAAC 59.140 45.455 0.00 0.00 0.00 2.43
2851 2985 5.559148 AAGGTTCAAAATTACATGGGCAA 57.441 34.783 0.00 0.00 0.00 4.52
2901 3035 4.290722 ACTGTTCTCCATTCTCCTCCATTT 59.709 41.667 0.00 0.00 0.00 2.32
3073 3207 9.701098 CACCTTACAAATTACTACAACTCTACA 57.299 33.333 0.00 0.00 0.00 2.74
3074 3208 9.702494 ACACCTTACAAATTACTACAACTCTAC 57.298 33.333 0.00 0.00 0.00 2.59
3076 3210 9.623000 AAACACCTTACAAATTACTACAACTCT 57.377 29.630 0.00 0.00 0.00 3.24
3119 3253 6.391227 AAACTGTACCACTTGAAATCTTGG 57.609 37.500 0.00 0.00 35.06 3.61
3164 3298 2.671396 CGTTAAGTGTGTGCCTCCATAC 59.329 50.000 0.00 0.00 34.09 2.39
3217 3351 5.623169 AGAACCTTAACAAAACCCGATGTA 58.377 37.500 0.00 0.00 0.00 2.29
3218 3352 4.466827 AGAACCTTAACAAAACCCGATGT 58.533 39.130 0.00 0.00 0.00 3.06
3320 3458 1.039856 GTGTGTTTTCCATGCAGGGT 58.960 50.000 18.43 0.00 38.24 4.34
3321 3459 1.000060 CTGTGTGTTTTCCATGCAGGG 60.000 52.381 12.23 12.23 38.24 4.45
3486 3624 9.791801 TGCCAGACATTAAGATATTATAGCAAA 57.208 29.630 0.00 0.00 0.00 3.68
3677 3818 7.959651 CAGAACAATGATTACTACTTCAACTGC 59.040 37.037 0.00 0.00 0.00 4.40
3800 3945 3.213206 TCTGCCACTTCAACTGATTGT 57.787 42.857 0.00 0.00 37.11 2.71
3807 3952 1.334869 CACCACTTCTGCCACTTCAAC 59.665 52.381 0.00 0.00 0.00 3.18
3905 4050 4.737765 GTCTAGCTGAAGAAATCTACTGCG 59.262 45.833 0.00 0.00 0.00 5.18
3956 4101 1.874019 CGCGTCTTCTGTCCATCGG 60.874 63.158 0.00 0.00 0.00 4.18
3960 4105 0.317160 AATCACGCGTCTTCTGTCCA 59.683 50.000 9.86 0.00 0.00 4.02
3974 4119 2.030805 GGCAACTCACACCAAGAATCAC 60.031 50.000 0.00 0.00 0.00 3.06
3979 4124 0.179020 CAGGGCAACTCACACCAAGA 60.179 55.000 0.00 0.00 0.00 3.02
3985 4130 0.465460 GGTGAACAGGGCAACTCACA 60.465 55.000 9.47 0.00 39.19 3.58
3986 4131 0.179018 AGGTGAACAGGGCAACTCAC 60.179 55.000 0.00 0.00 37.33 3.51
3987 4132 0.179020 CAGGTGAACAGGGCAACTCA 60.179 55.000 0.00 0.00 29.03 3.41
3990 4135 1.152756 ACCAGGTGAACAGGGCAAC 60.153 57.895 0.00 0.00 0.00 4.17
3995 4140 3.490348 AGAAATTGACCAGGTGAACAGG 58.510 45.455 0.00 0.00 0.00 4.00
4021 4166 3.066900 AGGAAGAACGTCGTGATCTATGG 59.933 47.826 0.00 0.00 0.00 2.74
4052 4197 2.496070 TGCCACGTCATCTTAAGCTAGT 59.504 45.455 0.00 0.00 0.00 2.57
4094 4239 6.377080 ACTACCATATCAGACCAGAAGATCA 58.623 40.000 0.00 0.00 0.00 2.92
4095 4240 6.909550 ACTACCATATCAGACCAGAAGATC 57.090 41.667 0.00 0.00 0.00 2.75
4122 4267 5.115472 GCACATCAGTAATTTGTTTCACGTG 59.885 40.000 9.94 9.94 0.00 4.49
4125 4270 5.117592 GCTGCACATCAGTAATTTGTTTCAC 59.882 40.000 0.00 0.00 44.66 3.18
4153 4298 2.355756 CAGAGAAATTACATGGCGGGTG 59.644 50.000 0.00 0.00 0.00 4.61
4158 4303 2.223665 GCAGGCAGAGAAATTACATGGC 60.224 50.000 0.00 0.00 36.75 4.40
4246 4404 7.527457 GGTGAAATTTACACTCATACCAGTTC 58.473 38.462 15.60 0.00 38.20 3.01
4247 4405 6.148811 CGGTGAAATTTACACTCATACCAGTT 59.851 38.462 15.60 0.00 38.20 3.16
4248 4406 5.642063 CGGTGAAATTTACACTCATACCAGT 59.358 40.000 15.60 0.00 38.20 4.00
4249 4407 5.642063 ACGGTGAAATTTACACTCATACCAG 59.358 40.000 15.60 0.00 38.20 4.00
4250 4408 5.553123 ACGGTGAAATTTACACTCATACCA 58.447 37.500 15.60 0.00 38.20 3.25
4251 4409 6.072893 ACAACGGTGAAATTTACACTCATACC 60.073 38.462 7.88 0.00 38.20 2.73
4252 4410 6.894828 ACAACGGTGAAATTTACACTCATAC 58.105 36.000 7.88 3.85 38.20 2.39
4253 4411 7.499321 AACAACGGTGAAATTTACACTCATA 57.501 32.000 7.88 0.00 38.20 2.15
4271 4429 6.345920 ACTTACAAGACTGAAGAAACAACG 57.654 37.500 0.00 0.00 0.00 4.10
4324 4482 1.528586 CAGGCACTTCAGTTGTTCGAG 59.471 52.381 0.00 0.00 34.60 4.04
4361 4519 0.109342 GGAGGTCGGGAATGCATCAT 59.891 55.000 0.00 0.00 0.00 2.45
4377 4535 4.630069 CGACAACATTTACCTACCTTGGAG 59.370 45.833 0.00 0.00 0.00 3.86
4383 4541 2.609350 TCGCGACAACATTTACCTACC 58.391 47.619 3.71 0.00 0.00 3.18
4384 4542 4.634991 CTTTCGCGACAACATTTACCTAC 58.365 43.478 9.15 0.00 0.00 3.18
4412 4573 4.506005 CCGCGCAATGTGGTACTA 57.494 55.556 8.75 0.00 43.63 1.82
4418 4579 1.440850 CACTGTTCCGCGCAATGTG 60.441 57.895 8.75 2.20 0.00 3.21
4419 4580 1.841663 GACACTGTTCCGCGCAATGT 61.842 55.000 8.75 0.00 0.00 2.71
4451 4612 1.073923 AGGGGGCAGAGTAAAAGTGTG 59.926 52.381 0.00 0.00 0.00 3.82
4453 4614 2.162681 CAAGGGGGCAGAGTAAAAGTG 58.837 52.381 0.00 0.00 0.00 3.16
4474 4635 6.748333 ATCACATTTGTGGAGTACATTCAG 57.252 37.500 10.60 0.00 45.65 3.02
4505 4666 4.134563 GCACTCCAAAAGAACCACTAGAA 58.865 43.478 0.00 0.00 0.00 2.10
4513 4674 3.128349 TCACTACGCACTCCAAAAGAAC 58.872 45.455 0.00 0.00 0.00 3.01
4526 4687 1.597663 CCCGGAATCAAATCACTACGC 59.402 52.381 0.73 0.00 0.00 4.42
4527 4688 2.864343 GTCCCGGAATCAAATCACTACG 59.136 50.000 0.73 0.00 0.00 3.51
4572 4733 1.334149 GCTTCACAACAAAGACTCCGC 60.334 52.381 0.00 0.00 0.00 5.54
4598 4759 2.094286 AGACACAAGAGATTCTGCTCCG 60.094 50.000 0.00 0.00 35.49 4.63
4599 4760 3.260740 CAGACACAAGAGATTCTGCTCC 58.739 50.000 0.00 0.00 35.49 4.70
4600 4761 3.924144 ACAGACACAAGAGATTCTGCTC 58.076 45.455 0.00 0.00 39.33 4.26
4601 4762 4.314121 GAACAGACACAAGAGATTCTGCT 58.686 43.478 0.00 0.00 39.33 4.24
4602 4763 3.434984 GGAACAGACACAAGAGATTCTGC 59.565 47.826 0.00 0.00 39.33 4.26
4612 4773 2.691526 AGTACGTGAGGAACAGACACAA 59.308 45.455 0.00 0.00 34.69 3.33
4618 4779 1.198408 TGCGTAGTACGTGAGGAACAG 59.802 52.381 22.81 0.00 44.73 3.16
4627 4788 3.313526 ACGATATTCCTTGCGTAGTACGT 59.686 43.478 22.81 4.88 44.73 3.57
4694 4861 8.130469 GCTAGTGGAGTACTATCTTTTCACTAC 58.870 40.741 0.00 0.00 40.94 2.73
4695 4862 7.012138 CGCTAGTGGAGTACTATCTTTTCACTA 59.988 40.741 0.00 0.00 40.94 2.74
4697 4864 5.972382 CGCTAGTGGAGTACTATCTTTTCAC 59.028 44.000 0.00 0.00 40.94 3.18
4698 4865 5.651139 ACGCTAGTGGAGTACTATCTTTTCA 59.349 40.000 8.42 0.00 40.94 2.69
4699 4866 5.972382 CACGCTAGTGGAGTACTATCTTTTC 59.028 44.000 8.42 0.00 44.34 2.29
4700 4867 5.892568 CACGCTAGTGGAGTACTATCTTTT 58.107 41.667 8.42 0.00 44.34 2.27
4734 4904 1.535437 GCATAAAGTCTGCTGCCATGC 60.535 52.381 0.00 0.00 36.68 4.06
4770 4940 8.281194 CGAGAATAAAGGAGTCAATTCATCATG 58.719 37.037 0.00 0.00 32.04 3.07
4778 4948 6.102663 CAGTGACGAGAATAAAGGAGTCAAT 58.897 40.000 0.00 0.00 39.80 2.57
4785 4955 5.060662 TCAGACAGTGACGAGAATAAAGG 57.939 43.478 0.00 0.00 0.00 3.11
4786 4956 5.944013 TCTCAGACAGTGACGAGAATAAAG 58.056 41.667 12.00 0.00 31.73 1.85
4787 4957 5.959618 TCTCAGACAGTGACGAGAATAAA 57.040 39.130 12.00 0.00 31.73 1.40
4792 4962 2.485814 CACATCTCAGACAGTGACGAGA 59.514 50.000 14.98 14.98 38.78 4.04
4808 4978 0.102120 CCTGAGACCGAGAGCACATC 59.898 60.000 0.00 0.00 0.00 3.06
4811 4981 1.214062 CACCTGAGACCGAGAGCAC 59.786 63.158 0.00 0.00 0.00 4.40
4819 4989 1.302832 CAGCAACCCACCTGAGACC 60.303 63.158 0.00 0.00 0.00 3.85
4855 5025 1.404035 TCAGACGACGTACATCATGGG 59.596 52.381 0.00 0.00 0.00 4.00
4858 5028 2.355132 GACCTCAGACGACGTACATCAT 59.645 50.000 0.00 0.00 0.00 2.45
4859 5029 1.736126 GACCTCAGACGACGTACATCA 59.264 52.381 0.00 0.00 0.00 3.07
4860 5030 2.008329 AGACCTCAGACGACGTACATC 58.992 52.381 0.00 0.00 0.00 3.06
4861 5031 1.738350 CAGACCTCAGACGACGTACAT 59.262 52.381 0.00 0.00 0.00 2.29
4862 5032 1.154197 CAGACCTCAGACGACGTACA 58.846 55.000 0.00 0.00 0.00 2.90
4863 5033 1.128321 GTCAGACCTCAGACGACGTAC 59.872 57.143 0.00 0.00 0.00 3.67
4864 5034 1.436600 GTCAGACCTCAGACGACGTA 58.563 55.000 0.00 0.00 0.00 3.57
4865 5035 1.235948 GGTCAGACCTCAGACGACGT 61.236 60.000 12.94 0.00 34.73 4.34
4866 5036 1.502640 GGTCAGACCTCAGACGACG 59.497 63.158 12.94 0.00 34.73 5.12


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

AutoCloner maintained by Alex Coulton.