Multiple sequence alignment - TraesCS2D01G274300

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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 TraesCS2D01G274300 chr2D 100.000 4735 0 0 2999 7733 342567220 342571954 0.000000e+00 8745.0
1 TraesCS2D01G274300 chr2D 100.000 2664 0 0 1 2664 342564222 342566885 0.000000e+00 4920.0
2 TraesCS2D01G274300 chr2D 90.066 302 23 4 7439 7733 526384000 526384301 1.220000e-102 385.0
3 TraesCS2D01G274300 chr2D 88.797 241 25 2 5210 5449 159321874 159322113 2.110000e-75 294.0
4 TraesCS2D01G274300 chr2D 79.598 348 52 14 5868 6208 619330919 619331254 1.680000e-56 231.0
5 TraesCS2D01G274300 chr2D 87.421 159 9 6 6985 7133 122864268 122864111 1.030000e-38 172.0
6 TraesCS2D01G274300 chr2D 97.297 37 1 0 6912 6948 342571091 342571127 6.480000e-06 63.9
7 TraesCS2D01G274300 chr2D 97.297 37 1 0 6870 6906 342571133 342571169 6.480000e-06 63.9
8 TraesCS2D01G274300 chr2A 95.625 2263 44 17 4226 6462 452795090 452797323 0.000000e+00 3579.0
9 TraesCS2D01G274300 chr2A 97.645 1444 30 3 123 1565 452786732 452788172 0.000000e+00 2475.0
10 TraesCS2D01G274300 chr2A 98.392 1244 19 1 2999 4242 452789619 452790861 0.000000e+00 2185.0
11 TraesCS2D01G274300 chr2A 97.488 1035 9 2 1629 2663 452788173 452789190 0.000000e+00 1751.0
12 TraesCS2D01G274300 chr2A 93.276 699 21 11 6574 7246 452797314 452798012 0.000000e+00 1007.0
13 TraesCS2D01G274300 chr2A 91.100 618 30 5 7140 7733 452798015 452798631 0.000000e+00 813.0
14 TraesCS2D01G274300 chr2A 89.712 243 18 7 5210 5449 170458238 170458476 3.510000e-78 303.0
15 TraesCS2D01G274300 chr2A 86.441 236 32 0 5214 5449 692710367 692710602 7.700000e-65 259.0
16 TraesCS2D01G274300 chr2A 100.000 123 0 0 1 123 452785807 452785929 2.170000e-55 228.0
17 TraesCS2D01G274300 chr2A 100.000 37 0 0 6912 6948 452797634 452797670 1.390000e-07 69.4
18 TraesCS2D01G274300 chr2A 97.297 37 1 0 6870 6906 452797676 452797712 6.480000e-06 63.9
19 TraesCS2D01G274300 chr2B 95.926 1399 44 10 1 1395 408081841 408083230 0.000000e+00 2255.0
20 TraesCS2D01G274300 chr2B 90.892 1614 66 23 5822 7366 408094626 408096227 0.000000e+00 2091.0
21 TraesCS2D01G274300 chr2B 95.614 912 24 4 1708 2605 408092277 408093186 0.000000e+00 1448.0
22 TraesCS2D01G274300 chr2B 94.725 455 12 6 3257 3705 408093819 408094267 0.000000e+00 697.0
23 TraesCS2D01G274300 chr2B 96.657 359 12 0 3742 4100 408094267 408094625 1.440000e-166 597.0
24 TraesCS2D01G274300 chr2B 91.724 290 17 3 7451 7733 486455621 486455332 5.620000e-106 396.0
25 TraesCS2D01G274300 chr2B 91.409 291 16 4 7451 7733 771297673 771297384 2.620000e-104 390.0
26 TraesCS2D01G274300 chr2B 89.695 262 3 7 3009 3267 408093186 408093426 5.830000e-81 313.0
27 TraesCS2D01G274300 chr2B 95.041 121 6 0 1391 1511 408091893 408092013 2.850000e-44 191.0
28 TraesCS2D01G274300 chr2B 88.542 96 5 5 1584 1678 408092186 408092276 2.280000e-20 111.0
29 TraesCS2D01G274300 chr2B 100.000 49 0 0 6912 6960 408095702 408095750 2.970000e-14 91.6
30 TraesCS2D01G274300 chr7D 91.753 291 17 2 7450 7733 472297775 472297485 1.560000e-106 398.0
31 TraesCS2D01G274300 chr6D 91.468 293 17 3 7449 7733 263589420 263589712 5.620000e-106 396.0
32 TraesCS2D01G274300 chr6D 91.379 290 18 2 7451 7733 4933696 4933985 2.620000e-104 390.0
33 TraesCS2D01G274300 chr1D 91.409 291 18 2 7450 7733 343343729 343344019 7.270000e-105 392.0
34 TraesCS2D01G274300 chr1D 91.003 289 20 2 7451 7733 137263974 137263686 1.220000e-102 385.0
35 TraesCS2D01G274300 chr1D 85.833 240 33 1 5211 5449 7770790 7770551 3.580000e-63 254.0
36 TraesCS2D01G274300 chr1D 92.373 118 7 2 7018 7133 273816278 273816395 4.800000e-37 167.0
37 TraesCS2D01G274300 chr4D 89.837 246 21 4 5210 5454 43054305 43054547 5.830000e-81 313.0
38 TraesCS2D01G274300 chr1B 84.274 248 37 2 5210 5456 611522968 611523214 2.790000e-59 241.0
39 TraesCS2D01G274300 chr5A 84.746 236 31 5 5213 5447 280727572 280727803 1.680000e-56 231.0
40 TraesCS2D01G274300 chr5A 84.167 240 37 1 5210 5449 567612083 567611845 1.680000e-56 231.0
41 TraesCS2D01G274300 chr5D 86.982 169 10 10 6981 7141 204323226 204323390 6.170000e-41 180.0
42 TraesCS2D01G274300 chr5D 87.261 157 10 4 6988 7134 285256710 285256866 3.710000e-38 171.0
43 TraesCS2D01G274300 chr5D 92.373 118 7 2 7018 7133 27353969 27353852 4.800000e-37 167.0
44 TraesCS2D01G274300 chr5B 86.982 169 10 10 6981 7141 208523293 208523457 6.170000e-41 180.0
45 TraesCS2D01G274300 chr3D 84.393 173 21 6 6976 7145 388793888 388793719 1.730000e-36 165.0
46 TraesCS2D01G274300 chr3D 90.323 124 10 2 7018 7139 535782553 535782676 2.230000e-35 161.0
47 TraesCS2D01G274300 chr3D 84.507 71 7 4 5800 5868 349138350 349138282 5.010000e-07 67.6
48 TraesCS2D01G274300 chr4B 100.000 28 0 0 5894 5921 449638814 449638841 1.400000e-02 52.8


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 TraesCS2D01G274300 chr2D 342564222 342571954 7732 False 3448.20 8745 98.64850 1 7733 4 chr2D.!!$F4 7732
1 TraesCS2D01G274300 chr2A 452785807 452790861 5054 False 1659.75 2475 98.38125 1 4242 4 chr2A.!!$F3 4241
2 TraesCS2D01G274300 chr2A 452795090 452798631 3541 False 1106.46 3579 95.45960 4226 7733 5 chr2A.!!$F4 3507
3 TraesCS2D01G274300 chr2B 408081841 408083230 1389 False 2255.00 2255 95.92600 1 1395 1 chr2B.!!$F1 1394
4 TraesCS2D01G274300 chr2B 408091893 408096227 4334 False 692.45 2091 93.89575 1391 7366 8 chr2B.!!$F2 5975

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
859 1667 4.095211 GGACTTTTAGTCTGGAGTAGGGT 58.905 47.826 6.77 0.00 44.46 4.34 F
1545 2455 0.684479 GTTCAGCAAATCCCTCCCCC 60.684 60.000 0.00 0.00 0.00 5.40 F
2608 3533 0.179020 ACGGGTGCATATGGACATGG 60.179 55.000 26.11 16.93 38.19 3.66 F
4430 5859 0.249489 AGCATCTGATTCGCGGTACC 60.249 55.000 6.13 0.16 0.00 3.34 F
5588 7039 0.321564 TTGAAGATGACACGGCAGGG 60.322 55.000 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2850 2.869503 ATTCACCCAGTAAGGCGCCG 62.870 60.0 23.20 7.32 35.39 6.46 R
3520 4943 0.954452 GCGTGATTGATTGGGGATCC 59.046 55.0 1.92 1.92 33.60 3.36 R
4533 5962 0.313672 CTCTGGCGAGTCTCTATGGC 59.686 60.0 0.00 0.00 32.47 4.40 R
5589 7040 0.455410 CTCTCTCACTGAAGAGCGGG 59.545 60.0 6.87 0.00 42.15 6.13 R
7436 9068 0.615331 TCAACAGGGCTAGCTTGGAG 59.385 55.0 15.72 10.19 0.00 3.86 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
294 1101 9.314133 TGCCTGTAAATGTATCTATCATCTAGT 57.686 33.333 0.00 0.00 0.00 2.57
568 1375 7.672983 TTTCTCTGTAGAAATGTAAAGCTGG 57.327 36.000 0.00 0.00 44.85 4.85
763 1571 5.180492 TCAAACGGTGCTTTTACTCTATTGG 59.820 40.000 0.00 0.00 0.00 3.16
859 1667 4.095211 GGACTTTTAGTCTGGAGTAGGGT 58.905 47.826 6.77 0.00 44.46 4.34
1164 1972 2.447244 AGAGCAAAGAGTTGAGACCG 57.553 50.000 0.00 0.00 36.83 4.79
1209 2017 4.764679 TTTGTTTCACTGCGATGCTTAT 57.235 36.364 0.00 0.00 0.00 1.73
1260 2068 2.972713 AGGTTGTAGAAGCAGTCCTGAA 59.027 45.455 4.50 0.00 31.56 3.02
1373 2181 0.973632 TTAAGGAGACAAGCCGAGCA 59.026 50.000 0.00 0.00 0.00 4.26
1545 2455 0.684479 GTTCAGCAAATCCCTCCCCC 60.684 60.000 0.00 0.00 0.00 5.40
1575 2485 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1578 2488 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1579 2489 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1580 2490 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1584 2494 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1587 2497 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1588 2498 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1589 2499 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1593 2503 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1594 2504 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1595 2505 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1596 2506 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1597 2507 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1598 2508 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1599 2509 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1600 2510 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1601 2511 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1607 2517 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
1608 2518 3.632333 TCTCTCTCTCTCTCTCTCTCGT 58.368 50.000 0.00 0.00 0.00 4.18
1617 2527 5.129650 TCTCTCTCTCTCTCGTCCTTATGAA 59.870 44.000 0.00 0.00 0.00 2.57
1620 2530 5.120399 TCTCTCTCTCGTCCTTATGAAGAC 58.880 45.833 0.00 0.00 0.00 3.01
1623 2533 3.948473 TCTCTCGTCCTTATGAAGACTGG 59.052 47.826 0.00 0.00 0.00 4.00
1688 2599 7.361031 GCTTGTTCAATCATCCAGAGCATATAG 60.361 40.741 0.00 0.00 0.00 1.31
1939 2850 5.897377 TTGCTCAGTTCCTTATAAAAGCC 57.103 39.130 0.00 0.00 0.00 4.35
2605 3530 1.271652 ACAAACGGGTGCATATGGACA 60.272 47.619 26.11 4.37 38.19 4.02
2607 3532 1.679139 AACGGGTGCATATGGACATG 58.321 50.000 26.11 19.60 38.19 3.21
2608 3533 0.179020 ACGGGTGCATATGGACATGG 60.179 55.000 26.11 16.93 38.19 3.66
2611 3536 1.411501 GGGTGCATATGGACATGGGTT 60.412 52.381 26.11 0.00 38.19 4.11
2612 3537 1.956477 GGTGCATATGGACATGGGTTC 59.044 52.381 26.11 5.83 38.19 3.62
2613 3538 2.653726 GTGCATATGGACATGGGTTCA 58.346 47.619 21.16 0.00 36.81 3.18
2614 3539 3.225104 GTGCATATGGACATGGGTTCAT 58.775 45.455 21.16 0.00 45.39 2.57
2615 3540 4.397420 GTGCATATGGACATGGGTTCATA 58.603 43.478 21.16 0.00 46.83 2.15
2663 3588 6.094048 CCTTAATCTTGTCATGTGGTGGTTAG 59.906 42.308 0.00 0.00 0.00 2.34
3462 4885 3.678056 TGTGCCTAGTTCTTGTGGTAG 57.322 47.619 0.00 0.00 0.00 3.18
3561 4985 5.060077 CGCTGCTGTCAGTTCAAAAATAATG 59.940 40.000 0.93 0.00 42.29 1.90
3630 5054 5.412904 GCAAAGGCTACACTATCTGAAACTT 59.587 40.000 0.00 0.00 36.96 2.66
3669 5097 3.772025 AGAATACTACCTGCAGTCAAGCT 59.228 43.478 13.81 0.00 34.99 3.74
4040 5468 5.921004 TTGTTTTGGTTTTATGCATCTGC 57.079 34.783 0.19 0.00 42.50 4.26
4169 5597 3.707793 TGGTGTTTTTATTTGTCGGCAC 58.292 40.909 0.00 0.00 0.00 5.01
4407 5836 2.039818 TTTGCTTCACCGTGTTACCA 57.960 45.000 0.00 0.00 0.00 3.25
4430 5859 0.249489 AGCATCTGATTCGCGGTACC 60.249 55.000 6.13 0.16 0.00 3.34
4477 5906 4.433615 GAGTGTTGATTTGGCGATCTCTA 58.566 43.478 0.00 0.00 0.00 2.43
4529 5958 4.250464 GGAATCGTACAACAGTGGATGAA 58.750 43.478 5.32 0.00 37.16 2.57
4530 5959 4.876107 GGAATCGTACAACAGTGGATGAAT 59.124 41.667 5.32 0.00 37.16 2.57
4531 5960 5.220662 GGAATCGTACAACAGTGGATGAATG 60.221 44.000 5.32 0.00 37.16 2.67
4532 5961 3.595173 TCGTACAACAGTGGATGAATGG 58.405 45.455 5.32 0.00 30.08 3.16
4533 5962 2.677836 CGTACAACAGTGGATGAATGGG 59.322 50.000 5.32 0.00 0.00 4.00
4534 5963 1.549203 ACAACAGTGGATGAATGGGC 58.451 50.000 5.32 0.00 0.00 5.36
4535 5964 0.819582 CAACAGTGGATGAATGGGCC 59.180 55.000 0.00 0.00 0.00 5.80
4536 5965 0.409092 AACAGTGGATGAATGGGCCA 59.591 50.000 9.61 9.61 0.00 5.36
4537 5966 0.632835 ACAGTGGATGAATGGGCCAT 59.367 50.000 14.78 14.78 33.66 4.40
4538 5967 1.852309 ACAGTGGATGAATGGGCCATA 59.148 47.619 21.54 5.24 33.66 2.74
4539 5968 2.158564 ACAGTGGATGAATGGGCCATAG 60.159 50.000 21.54 4.14 33.66 2.23
4540 5969 2.107031 CAGTGGATGAATGGGCCATAGA 59.893 50.000 21.54 9.79 33.66 1.98
4741 6170 4.200283 GAGCGGAGGTGGAGCTCG 62.200 72.222 7.83 0.00 46.14 5.03
4817 6246 0.749818 TCAAACGTGTGTGCATGGGT 60.750 50.000 5.45 0.00 35.99 4.51
4958 6387 1.141881 AAGGGCTGCTATGACGTCG 59.858 57.895 11.62 0.00 0.00 5.12
5130 6581 1.961133 TTTATTCCAGGGGAGGTCGT 58.039 50.000 0.00 0.00 31.21 4.34
5144 6595 2.355363 TCGTTTCGGTGTGAGGCG 60.355 61.111 0.00 0.00 0.00 5.52
5154 6605 4.803426 GTGAGGCGGTGGAGCTCG 62.803 72.222 7.83 0.00 37.29 5.03
5169 6620 1.559682 AGCTCGGTGGTGGACATTAAT 59.440 47.619 0.00 0.00 0.00 1.40
5176 6627 0.738389 GGTGGACATTAATGGCGTGG 59.262 55.000 19.37 0.00 36.40 4.94
5197 6648 0.664166 CAATCCGCGGCCATTAATGC 60.664 55.000 23.51 5.72 0.00 3.56
5222 6673 2.128771 TAAGGCGTACTACCTCCGTT 57.871 50.000 4.90 0.00 36.14 4.44
5234 6685 1.624813 ACCTCCGTTCGGGTTTATTGA 59.375 47.619 11.37 0.00 37.00 2.57
5339 6790 6.627395 TGGATTCGTGTTTGAACATAGTTT 57.373 33.333 0.00 0.00 41.59 2.66
5436 6887 2.104281 CGAGGGGGACTAATAAACCAGG 59.896 54.545 0.00 0.00 0.00 4.45
5439 6890 2.848071 GGGGGACTAATAAACCAGGACA 59.152 50.000 0.00 0.00 0.00 4.02
5466 6917 2.866454 AGTAGTATGGAGGGGAGAGGTT 59.134 50.000 0.00 0.00 0.00 3.50
5523 6974 1.843206 GCCTGAGAGAGGAAGGGAAAT 59.157 52.381 0.00 0.00 46.33 2.17
5538 6989 1.304381 AAATGGCAGCCATCGTGGT 60.304 52.632 27.82 8.69 44.40 4.16
5541 6992 3.127533 GGCAGCCATCGTGGTGTC 61.128 66.667 6.55 0.00 40.46 3.67
5571 7022 3.353836 CGACGTTGGCTGGGGTTG 61.354 66.667 0.00 0.00 0.00 3.77
5588 7039 0.321564 TTGAAGATGACACGGCAGGG 60.322 55.000 0.00 0.00 0.00 4.45
5589 7040 2.045926 AAGATGACACGGCAGGGC 60.046 61.111 0.00 0.00 0.00 5.19
5590 7041 3.628646 AAGATGACACGGCAGGGCC 62.629 63.158 0.00 0.00 46.75 5.80
6117 7573 5.083533 ACTTGTTTGACATGGCTTGAAAA 57.916 34.783 7.45 4.93 0.00 2.29
6248 7704 7.611467 ACATATATTGAAAGCCTTGAGACACAA 59.389 33.333 0.00 0.00 36.97 3.33
6261 7717 2.162408 GAGACACAACTATTGGCAAGCC 59.838 50.000 5.96 3.61 34.12 4.35
6512 7970 1.312815 AACCAACTCAGAGCTGCAAC 58.687 50.000 1.02 0.00 0.00 4.17
6546 8004 6.812160 GGTCCATCCTGATTTATCGTGTATAC 59.188 42.308 0.00 0.00 0.00 1.47
6547 8005 7.375834 GTCCATCCTGATTTATCGTGTATACA 58.624 38.462 0.08 0.08 0.00 2.29
6558 8016 1.404391 CGTGTATACAGGCTTCTCGGT 59.596 52.381 12.28 0.00 0.00 4.69
6612 8070 4.464597 GCCTCGGGATTCAGAGATAACTAT 59.535 45.833 2.21 0.00 36.65 2.12
6710 8192 2.402238 ACCATGGCAGGTCCTTGAT 58.598 52.632 13.04 0.00 41.25 2.57
6779 8263 4.441913 CCACAAGAACCATGAAGCAAAACT 60.442 41.667 0.00 0.00 0.00 2.66
6902 8386 6.317893 TGTGGGAAGTAACTTTGAAGAACTTC 59.682 38.462 21.70 21.70 43.53 3.01
7075 8575 8.345565 AGTATGTTTGTTCACTCATTTCAGTTC 58.654 33.333 0.00 0.00 0.00 3.01
7076 8576 6.507958 TGTTTGTTCACTCATTTCAGTTCA 57.492 33.333 0.00 0.00 0.00 3.18
7092 8592 9.645059 ATTTCAGTTCATATGTAGTCCATATCG 57.355 33.333 1.90 0.00 43.46 2.92
7168 8668 2.093288 CCTTGCTGCAGGACTTGATAGA 60.093 50.000 17.12 0.00 35.71 1.98
7176 8676 8.815912 TGCTGCAGGACTTGATAGAAATATATA 58.184 33.333 17.12 0.00 0.00 0.86
7417 9049 6.540438 ACTTAATACGGGAGAAGAACATCA 57.460 37.500 0.00 0.00 0.00 3.07
7436 9068 6.108015 ACATCATTTTGCATATGTTCCAACC 58.892 36.000 4.29 0.00 0.00 3.77
7449 9081 1.077429 CCAACCTCCAAGCTAGCCC 60.077 63.158 12.13 0.00 0.00 5.19
7451 9083 0.393537 CAACCTCCAAGCTAGCCCTG 60.394 60.000 12.13 9.31 0.00 4.45
7452 9084 0.842467 AACCTCCAAGCTAGCCCTGT 60.842 55.000 12.13 0.00 0.00 4.00
7469 9125 4.392940 CCCTGTTGAAATATGCCCTAGAG 58.607 47.826 0.00 0.00 0.00 2.43
7632 9288 7.584987 AGTTCGTTCATCAAAAGATGGTTAAG 58.415 34.615 5.71 0.00 33.61 1.85
7639 9295 7.010160 TCATCAAAAGATGGTTAAGGTTTCCT 58.990 34.615 5.71 0.00 32.16 3.36
7649 9305 5.183969 GGTTAAGGTTTCCTGACCATAGAC 58.816 45.833 13.27 0.00 42.35 2.59
7710 9366 5.440610 AGAATGATGTAATGGACAAGACCC 58.559 41.667 0.00 0.00 42.78 4.46
7711 9367 3.260475 TGATGTAATGGACAAGACCCG 57.740 47.619 0.00 0.00 42.78 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 1068 9.937175 GATAGATACATTTACAGGCAAAAACTC 57.063 33.333 0.00 0.00 0.00 3.01
294 1101 1.042003 TGCACGTATAACCCGGCCTA 61.042 55.000 0.00 0.00 0.00 3.93
615 1422 5.325239 AGGAAAAACTACATAGGCAGCTTT 58.675 37.500 0.00 0.00 0.00 3.51
763 1571 7.088589 AGTCATTCATAATTTGTACCAGTGC 57.911 36.000 0.00 0.00 0.00 4.40
859 1667 3.751175 GGATACAAACAAGTGCAGCTACA 59.249 43.478 0.00 0.00 0.00 2.74
1164 1972 3.706055 TCCAGAAGGAACACTGTGC 57.294 52.632 7.90 0.00 42.23 4.57
1209 2017 3.436704 GCTCACCGTTGATCAATTTCTCA 59.563 43.478 12.12 0.00 0.00 3.27
1260 2068 8.371699 GGTATCATTTTATAGTCCTCTGAAGCT 58.628 37.037 0.00 0.00 0.00 3.74
1545 2455 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1546 2456 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1575 2485 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1578 2488 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1579 2489 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1580 2490 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1584 2494 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
1587 2497 3.632333 ACGAGAGAGAGAGAGAGAGAGA 58.368 50.000 0.00 0.00 0.00 3.10
1588 2498 3.243569 GGACGAGAGAGAGAGAGAGAGAG 60.244 56.522 0.00 0.00 0.00 3.20
1589 2499 2.693591 GGACGAGAGAGAGAGAGAGAGA 59.306 54.545 0.00 0.00 0.00 3.10
1593 2503 4.651962 TCATAAGGACGAGAGAGAGAGAGA 59.348 45.833 0.00 0.00 0.00 3.10
1594 2504 4.956085 TCATAAGGACGAGAGAGAGAGAG 58.044 47.826 0.00 0.00 0.00 3.20
1595 2505 5.129650 TCTTCATAAGGACGAGAGAGAGAGA 59.870 44.000 0.00 0.00 0.00 3.10
1596 2506 5.236478 GTCTTCATAAGGACGAGAGAGAGAG 59.764 48.000 0.00 0.00 0.00 3.20
1597 2507 5.104693 AGTCTTCATAAGGACGAGAGAGAGA 60.105 44.000 0.00 0.00 37.52 3.10
1598 2508 5.007626 CAGTCTTCATAAGGACGAGAGAGAG 59.992 48.000 0.00 0.00 37.52 3.20
1599 2509 4.878971 CAGTCTTCATAAGGACGAGAGAGA 59.121 45.833 0.00 0.00 37.52 3.10
1600 2510 4.036262 CCAGTCTTCATAAGGACGAGAGAG 59.964 50.000 0.00 0.00 37.52 3.20
1601 2511 3.948473 CCAGTCTTCATAAGGACGAGAGA 59.052 47.826 0.00 0.00 37.52 3.10
1607 2517 5.105310 TGCTTCTACCAGTCTTCATAAGGAC 60.105 44.000 0.00 0.00 0.00 3.85
1608 2518 5.023452 TGCTTCTACCAGTCTTCATAAGGA 58.977 41.667 0.00 0.00 0.00 3.36
1617 2527 4.130118 CTGTTTGTTGCTTCTACCAGTCT 58.870 43.478 0.00 0.00 0.00 3.24
1620 2530 3.876914 TGTCTGTTTGTTGCTTCTACCAG 59.123 43.478 0.00 0.00 0.00 4.00
1623 2533 7.639945 ACTTATTGTCTGTTTGTTGCTTCTAC 58.360 34.615 0.00 0.00 0.00 2.59
1893 2804 5.751586 TCAGTCTAACCAATTGTATTCCCC 58.248 41.667 4.43 0.00 0.00 4.81
1939 2850 2.869503 ATTCACCCAGTAAGGCGCCG 62.870 60.000 23.20 7.32 35.39 6.46
2605 3530 5.289510 AGGGAAAGTCTAGTATGAACCCAT 58.710 41.667 0.00 0.00 37.49 4.00
2607 3532 4.963628 AGAGGGAAAGTCTAGTATGAACCC 59.036 45.833 0.00 0.00 35.53 4.11
2608 3533 7.842887 ATAGAGGGAAAGTCTAGTATGAACC 57.157 40.000 0.00 0.00 30.04 3.62
2613 3538 9.590828 GGTTCTTATAGAGGGAAAGTCTAGTAT 57.409 37.037 0.00 0.00 30.04 2.12
2614 3539 8.789782 AGGTTCTTATAGAGGGAAAGTCTAGTA 58.210 37.037 0.00 0.00 30.04 1.82
2615 3540 7.654452 AGGTTCTTATAGAGGGAAAGTCTAGT 58.346 38.462 0.00 0.00 30.04 2.57
3006 4024 4.153117 CGGAATGAGTGAAAAACAGAGGAG 59.847 45.833 0.00 0.00 0.00 3.69
3462 4885 5.182001 ACAGGCAACACTCAGAATCAATTAC 59.818 40.000 0.00 0.00 41.41 1.89
3520 4943 0.954452 GCGTGATTGATTGGGGATCC 59.046 55.000 1.92 1.92 33.60 3.36
3601 5025 4.937620 CAGATAGTGTAGCCTTTGCAGAAA 59.062 41.667 0.00 0.00 41.13 2.52
3630 5054 7.750229 AGTATTCTGATTTCAAAGTCAGCAA 57.250 32.000 9.65 6.53 41.21 3.91
3709 5137 6.544038 AGCATTTCCAATACAAGCAAAAAC 57.456 33.333 0.00 0.00 0.00 2.43
3913 5341 2.370519 TCGACCTGAAAAGAATGTCCCA 59.629 45.455 0.00 0.00 0.00 4.37
4040 5468 9.760660 GTTGACTGCAAAACTTATAACTCATAG 57.239 33.333 0.00 0.00 35.42 2.23
4169 5597 3.182967 GCAACGACAACTAGATCTGGAG 58.817 50.000 13.73 7.36 0.00 3.86
4407 5836 1.886313 CGCGAATCAGATGCTGCCT 60.886 57.895 0.00 0.00 0.00 4.75
4430 5859 5.061808 CCAGTTAACTCACTTAACCGAATCG 59.938 44.000 4.77 0.00 43.80 3.34
4477 5906 6.521527 AGGGCCAGATTAGATCACTTAAAT 57.478 37.500 6.18 0.00 0.00 1.40
4504 5933 1.724623 CCACTGTTGTACGATTCCACG 59.275 52.381 0.00 0.00 39.31 4.94
4506 5935 3.259625 TCATCCACTGTTGTACGATTCCA 59.740 43.478 0.00 0.00 0.00 3.53
4529 5958 1.476007 GGCGAGTCTCTATGGCCCAT 61.476 60.000 0.00 0.00 37.82 4.00
4530 5959 2.134287 GGCGAGTCTCTATGGCCCA 61.134 63.158 0.00 0.00 37.82 5.36
4531 5960 2.093537 CTGGCGAGTCTCTATGGCCC 62.094 65.000 12.37 0.00 43.09 5.80
4532 5961 1.109920 TCTGGCGAGTCTCTATGGCC 61.110 60.000 9.00 9.00 44.00 5.36
4533 5962 0.313672 CTCTGGCGAGTCTCTATGGC 59.686 60.000 0.00 0.00 32.47 4.40
4534 5963 1.879380 CTCTCTGGCGAGTCTCTATGG 59.121 57.143 0.00 0.00 38.45 2.74
4535 5964 1.879380 CCTCTCTGGCGAGTCTCTATG 59.121 57.143 0.00 0.00 38.45 2.23
4536 5965 1.771854 TCCTCTCTGGCGAGTCTCTAT 59.228 52.381 0.00 0.00 38.45 1.98
4537 5966 1.205055 TCCTCTCTGGCGAGTCTCTA 58.795 55.000 0.00 0.00 38.45 2.43
4538 5967 0.329931 TTCCTCTCTGGCGAGTCTCT 59.670 55.000 0.00 0.00 38.45 3.10
4539 5968 1.178276 TTTCCTCTCTGGCGAGTCTC 58.822 55.000 0.00 0.00 38.45 3.36
4540 5969 1.273886 GTTTTCCTCTCTGGCGAGTCT 59.726 52.381 0.00 0.00 38.45 3.24
4667 6096 3.196039 GGACCTCCCAAGTTCTCTAAGAC 59.804 52.174 0.00 0.00 34.14 3.01
4741 6170 1.591327 CACGCAAACCACAAAGCCC 60.591 57.895 0.00 0.00 0.00 5.19
4817 6246 2.008400 TCCTCCTTTCCCTCTACCTCA 58.992 52.381 0.00 0.00 0.00 3.86
4859 6288 0.456221 CTCCACATACGACGAAGCCT 59.544 55.000 0.00 0.00 0.00 4.58
4958 6387 1.153549 ATCCGACGAAGCTTGCCTC 60.154 57.895 2.10 0.00 0.00 4.70
5100 6551 1.062587 CTGGAATAAAAGGCGCACTCG 59.937 52.381 10.83 0.00 39.07 4.18
5130 6581 2.280524 CACCGCCTCACACCGAAA 60.281 61.111 0.00 0.00 0.00 3.46
5144 6595 4.394712 CCACCACCGAGCTCCACC 62.395 72.222 8.47 0.00 0.00 4.61
5154 6605 0.738389 CGCCATTAATGTCCACCACC 59.262 55.000 14.25 0.00 0.00 4.61
5176 6627 0.951558 ATTAATGGCCGCGGATTGAC 59.048 50.000 33.48 10.82 0.00 3.18
5234 6685 1.388837 GCACAAAACACGAAGGGGGT 61.389 55.000 0.00 0.00 0.00 4.95
5301 6752 8.706492 ACACGAATCCAACGATATAGTTTTTA 57.294 30.769 0.00 0.00 30.96 1.52
5425 6876 7.416731 ACTACTACCTCTGTCCTGGTTTATTA 58.583 38.462 0.00 0.00 37.74 0.98
5436 6887 4.400120 CCCTCCATACTACTACCTCTGTC 58.600 52.174 0.00 0.00 0.00 3.51
5439 6890 3.658705 CTCCCCTCCATACTACTACCTCT 59.341 52.174 0.00 0.00 0.00 3.69
5523 6974 3.899981 GACACCACGATGGCTGCCA 62.900 63.158 25.65 25.65 42.67 4.92
5571 7022 2.109126 GCCCTGCCGTGTCATCTTC 61.109 63.158 0.00 0.00 0.00 2.87
5588 7039 1.153667 CTCTCACTGAAGAGCGGGC 60.154 63.158 0.00 0.00 36.64 6.13
5589 7040 0.455410 CTCTCTCACTGAAGAGCGGG 59.545 60.000 6.87 0.00 42.15 6.13
5590 7041 0.455410 CCTCTCTCACTGAAGAGCGG 59.545 60.000 10.48 6.50 40.77 5.52
5591 7042 0.455410 CCCTCTCTCACTGAAGAGCG 59.545 60.000 10.48 2.35 42.15 5.03
5705 7158 9.847224 ACTAGAAAAGAAATAACCAGAAACAGA 57.153 29.630 0.00 0.00 0.00 3.41
5787 7240 3.530265 AATGATTTTGCCGATGTGCAT 57.470 38.095 0.00 0.00 41.70 3.96
6088 7544 3.742369 GCCATGTCAAACAAGTTGGATTG 59.258 43.478 7.96 11.81 37.85 2.67
6214 7670 8.849168 CAAGGCTTTCAATATATGTAACATCCA 58.151 33.333 0.00 0.00 0.00 3.41
6248 7704 2.128771 AACATCGGCTTGCCAATAGT 57.871 45.000 12.45 1.75 0.00 2.12
6261 7717 1.278238 GAGGTACGAGCCAAACATCG 58.722 55.000 0.00 0.00 44.36 3.84
6321 7777 5.425217 TGGATTAGCTTGTGAGGAACATAGA 59.575 40.000 0.00 0.00 38.99 1.98
6512 7970 4.225497 GGATGGACCTTGAAGCCG 57.775 61.111 0.00 0.00 35.41 5.52
6546 8004 1.068954 GCTTGAAAACCGAGAAGCCTG 60.069 52.381 0.00 0.00 35.76 4.85
6547 8005 1.239347 GCTTGAAAACCGAGAAGCCT 58.761 50.000 0.00 0.00 35.76 4.58
6577 8035 1.142314 CCGAGGCATTTTGCATGGG 59.858 57.895 0.96 0.96 45.64 4.00
6612 8070 2.357637 CAGAAGGAACACGGAAAAGCAA 59.642 45.455 0.00 0.00 0.00 3.91
6710 8192 3.603965 ACCACAAACCCTTGAACCATA 57.396 42.857 0.00 0.00 36.33 2.74
6779 8263 3.181445 ACCAGTCACATGTTAAGGCAGAA 60.181 43.478 0.00 0.00 0.00 3.02
6784 8268 4.641396 TCTGAACCAGTCACATGTTAAGG 58.359 43.478 0.00 0.00 32.61 2.69
6902 8386 7.123247 ACTTCCCACATTCTTCCAAGATTATTG 59.877 37.037 0.00 0.00 34.49 1.90
7176 8676 9.793252 GTTACATGTAAGCAAATCTCATTGATT 57.207 29.630 18.56 0.00 46.49 2.57
7391 9023 8.533657 TGATGTTCTTCTCCCGTATTAAGTTAA 58.466 33.333 0.00 0.00 0.00 2.01
7403 9035 4.789012 TGCAAAATGATGTTCTTCTCCC 57.211 40.909 0.00 0.00 0.00 4.30
7404 9036 7.486647 ACATATGCAAAATGATGTTCTTCTCC 58.513 34.615 16.80 0.00 0.00 3.71
7417 9049 4.776837 TGGAGGTTGGAACATATGCAAAAT 59.223 37.500 1.58 0.00 41.36 1.82
7436 9068 0.615331 TCAACAGGGCTAGCTTGGAG 59.385 55.000 15.72 10.19 0.00 3.86
7528 9184 8.795842 AGTTTCCGACCAATACAATTATAACA 57.204 30.769 0.00 0.00 0.00 2.41
7544 9200 7.124347 TCACACATGTATTTAAGTTTCCGAC 57.876 36.000 0.00 0.00 0.00 4.79
7632 9288 4.080863 ACTCATGTCTATGGTCAGGAAACC 60.081 45.833 0.00 0.00 39.94 3.27
7685 9341 6.352516 GGTCTTGTCCATTACATCATTCTCT 58.647 40.000 0.00 0.00 38.10 3.10
7710 9366 3.833442 TCATATGCTATGCTAACGGACG 58.167 45.455 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.