Multiple sequence alignment - TraesCS7B01G166600

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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 TraesCS7B01G166600 chr7B 100.000 4701 0 0 1 4701 229868500 229873200 0.000000e+00 8682.0
1 TraesCS7B01G166600 chr7B 91.266 229 17 2 971 1199 300322564 300322789 4.570000e-80 309.0
2 TraesCS7B01G166600 chr7A 91.323 4241 224 52 1 4161 267434187 267430011 0.000000e+00 5661.0
3 TraesCS7B01G166600 chr7A 90.108 556 52 3 4148 4701 267397729 267397175 0.000000e+00 719.0
4 TraesCS7B01G166600 chr7A 93.886 229 11 2 971 1199 227064578 227064803 4.500000e-90 342.0
5 TraesCS7B01G166600 chr7D 93.898 3163 111 33 873 3963 252557157 252560309 0.000000e+00 4697.0
6 TraesCS7B01G166600 chr7D 87.045 741 55 19 118 840 252556442 252557159 0.000000e+00 798.0
7 TraesCS7B01G166600 chr7D 87.342 158 17 3 4546 4701 618162753 618162909 1.340000e-40 178.0
8 TraesCS7B01G166600 chr7D 86.624 157 20 1 4546 4701 301993791 301993947 6.250000e-39 172.0
9 TraesCS7B01G166600 chr7D 85.897 156 19 3 4547 4701 385583882 385584035 3.760000e-36 163.0
10 TraesCS7B01G166600 chr7D 88.991 109 7 4 1 109 252554988 252555091 3.820000e-26 130.0
11 TraesCS7B01G166600 chr1A 91.640 622 51 1 1865 2486 406627343 406627963 0.000000e+00 859.0
12 TraesCS7B01G166600 chr1A 90.000 640 62 2 1865 2503 425075823 425075185 0.000000e+00 826.0
13 TraesCS7B01G166600 chr5A 82.609 299 46 5 1074 1369 514093327 514093622 4.670000e-65 259.0
14 TraesCS7B01G166600 chr5A 93.750 80 1 2 1645 1723 554116147 554116071 2.970000e-22 117.0
15 TraesCS7B01G166600 chr5A 85.897 78 10 1 992 1068 514093196 514093273 1.080000e-11 82.4
16 TraesCS7B01G166600 chr5B 87.261 157 17 3 4547 4701 347380510 347380665 4.830000e-40 176.0
17 TraesCS7B01G166600 chr4D 86.624 157 19 2 4547 4701 132136114 132136270 6.250000e-39 172.0
18 TraesCS7B01G166600 chr4D 85.987 157 20 2 4546 4701 407771455 407771610 2.910000e-37 167.0
19 TraesCS7B01G166600 chr3D 86.624 157 20 1 4546 4701 608738285 608738129 6.250000e-39 172.0
20 TraesCS7B01G166600 chr4A 86.624 157 18 3 4547 4701 57127903 57127748 2.250000e-38 171.0
21 TraesCS7B01G166600 chr2D 93.750 80 1 2 1645 1723 420721737 420721813 2.970000e-22 117.0
22 TraesCS7B01G166600 chr1B 93.750 80 1 2 1645 1723 200415432 200415508 2.970000e-22 117.0
23 TraesCS7B01G166600 chr5D 86.765 68 9 0 1001 1068 408301163 408301230 5.040000e-10 76.8


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 TraesCS7B01G166600 chr7B 229868500 229873200 4700 False 8682 8682 100.000 1 4701 1 chr7B.!!$F1 4700
1 TraesCS7B01G166600 chr7A 267430011 267434187 4176 True 5661 5661 91.323 1 4161 1 chr7A.!!$R2 4160
2 TraesCS7B01G166600 chr7A 267397175 267397729 554 True 719 719 90.108 4148 4701 1 chr7A.!!$R1 553
3 TraesCS7B01G166600 chr7D 252554988 252560309 5321 False 1875 4697 89.978 1 3963 3 chr7D.!!$F4 3962
4 TraesCS7B01G166600 chr1A 406627343 406627963 620 False 859 859 91.640 1865 2486 1 chr1A.!!$F1 621
5 TraesCS7B01G166600 chr1A 425075185 425075823 638 True 826 826 90.000 1865 2503 1 chr1A.!!$R1 638

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
921 2303 0.111639 TTGGTGAGGCAAGGGGTTAC 59.888 55.000 0.00 0.0 0.00 2.50 F
1017 2399 0.546267 ACATGGAGAGGCAGACCAGT 60.546 55.000 0.00 0.0 39.06 4.00 F
1624 3010 1.133976 AGTGCTAACATCTGGCCATCC 60.134 52.381 5.51 0.0 0.00 3.51 F
2187 3578 1.442526 CCGATGCTAGCCTTGCCAAG 61.443 60.000 13.29 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3560 0.462581 TCTTGGCAAGGCTAGCATCG 60.463 55.000 25.92 0.0 0.00 3.84 R
2959 4412 0.521735 CCGGCTCTTTTGCAGTTACC 59.478 55.000 0.00 0.0 34.04 2.85 R
3310 4763 1.591059 CGAGATGAAGAGCGCCAGG 60.591 63.158 2.29 0.0 0.00 4.45 R
3999 5453 0.523072 TACACCGTTGGCGTACTCTC 59.477 55.000 0.00 0.0 36.15 3.20 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
71 72 9.436957 AGTTTGAACGACAATTAATATGAGACT 57.563 29.630 0.00 0.00 38.36 3.24
78 79 6.479990 CGACAATTAATATGAGACTGAGGCAA 59.520 38.462 0.00 0.00 0.00 4.52
110 111 6.866770 ACAATACCTTACCGTTATCATCATCG 59.133 38.462 0.00 0.00 0.00 3.84
111 112 4.931661 ACCTTACCGTTATCATCATCGT 57.068 40.909 0.00 0.00 0.00 3.73
224 1572 4.495472 CCAACTTGCGCAGTTAATTATTCG 59.505 41.667 19.88 9.05 44.60 3.34
265 1613 0.532862 CGTGCTGTCTTCACTTGGGT 60.533 55.000 0.00 0.00 32.54 4.51
354 1703 9.528018 CCAACAAACAAGAAGAATAAAAGCTAA 57.472 29.630 0.00 0.00 0.00 3.09
356 1705 9.750125 AACAAACAAGAAGAATAAAAGCTAAGG 57.250 29.630 0.00 0.00 0.00 2.69
510 1866 2.798976 TCATTTCTTTGGTGCACTGC 57.201 45.000 17.98 0.83 0.00 4.40
537 1893 2.094390 GGGGCGAAATTGGTAAGGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
542 1898 6.406512 GGGCGAAATTGGTAAGGTTTCATATT 60.407 38.462 0.00 0.00 32.75 1.28
621 1986 3.594603 TCTTCGGTTCTTGGAGATGTC 57.405 47.619 0.00 0.00 0.00 3.06
702 2067 2.012673 CCTTTGCAGTATCAGGTGCTC 58.987 52.381 0.00 0.00 40.54 4.26
716 2081 1.001764 TGCTCTGTTCATGGCCCAG 60.002 57.895 0.00 0.00 0.00 4.45
731 2096 1.342975 GCCCAGGGGTATTGATTGGTT 60.343 52.381 7.91 0.00 37.65 3.67
771 2136 1.595109 GTTTTGTGCAAGGCAGCCC 60.595 57.895 8.22 0.00 40.08 5.19
811 2179 5.242615 AGAGAAGGCAAGTCTTGGATTTTTC 59.757 40.000 14.40 0.00 0.00 2.29
812 2180 4.281941 AGAAGGCAAGTCTTGGATTTTTCC 59.718 41.667 14.40 5.06 0.00 3.13
836 2204 2.111384 TCACAATCTCAGGTCCCTAGC 58.889 52.381 0.00 0.00 0.00 3.42
844 2212 1.354031 TCAGGTCCCTAGCAATTGCAA 59.646 47.619 30.89 0.00 45.16 4.08
847 2215 3.026694 AGGTCCCTAGCAATTGCAAATC 58.973 45.455 30.89 15.38 45.16 2.17
851 2219 2.101917 CCCTAGCAATTGCAAATCAGGG 59.898 50.000 30.89 27.94 45.16 4.45
860 2228 0.686789 GCAAATCAGGGGGCTTGTTT 59.313 50.000 0.00 0.00 0.00 2.83
862 2230 2.487086 GCAAATCAGGGGGCTTGTTTTT 60.487 45.455 0.00 0.00 0.00 1.94
921 2303 0.111639 TTGGTGAGGCAAGGGGTTAC 59.888 55.000 0.00 0.00 0.00 2.50
922 2304 1.001269 GGTGAGGCAAGGGGTTACC 60.001 63.158 0.00 0.00 40.67 2.85
933 2315 1.100510 GGGGTTACCTGGATTTTCGC 58.899 55.000 0.00 0.00 36.80 4.70
934 2316 1.614850 GGGGTTACCTGGATTTTCGCA 60.615 52.381 0.00 0.00 36.80 5.10
952 2334 1.600023 CAAGAACAGGGGCGTTACAA 58.400 50.000 0.00 0.00 0.00 2.41
996 2378 2.893489 GTCCAGTTGATTCTTGGGCTTT 59.107 45.455 0.00 0.00 0.00 3.51
1017 2399 0.546267 ACATGGAGAGGCAGACCAGT 60.546 55.000 0.00 0.00 39.06 4.00
1065 2447 2.770048 AGCTTCCGGGGGATGGAG 60.770 66.667 0.00 0.00 36.72 3.86
1347 2729 3.195698 GACGCCTTCCACATCGCC 61.196 66.667 0.00 0.00 0.00 5.54
1382 2764 3.140325 TCTGGGTAAGCTGTTTTCCTG 57.860 47.619 0.00 0.15 0.00 3.86
1383 2765 2.441750 TCTGGGTAAGCTGTTTTCCTGT 59.558 45.455 0.00 0.00 0.00 4.00
1447 2830 5.393461 CCAAGCCTGTGAAATGATTCCTTAC 60.393 44.000 0.00 0.00 34.49 2.34
1484 2867 3.389002 AGGATTTGGGCATAGATTTTGGC 59.611 43.478 0.00 0.00 38.82 4.52
1502 2885 1.363744 GCGCAGTGAGTAGATTGCTT 58.636 50.000 0.30 0.00 34.50 3.91
1544 2930 7.443575 CCTATTCTTATCTGATTGAGTTGGTGG 59.556 40.741 0.00 0.00 0.00 4.61
1551 2937 4.469586 TCTGATTGAGTTGGTGGCATAGTA 59.530 41.667 0.00 0.00 0.00 1.82
1554 2940 5.423931 TGATTGAGTTGGTGGCATAGTAGTA 59.576 40.000 0.00 0.00 0.00 1.82
1561 2947 3.699538 TGGTGGCATAGTAGTACTCACAG 59.300 47.826 17.10 5.07 0.00 3.66
1624 3010 1.133976 AGTGCTAACATCTGGCCATCC 60.134 52.381 5.51 0.00 0.00 3.51
1743 3130 2.095461 TCTGTAGCACTAGCAGTCCTG 58.905 52.381 0.00 0.00 45.49 3.86
1945 3334 4.294416 AGTGGAGATCGAATTACAGTCG 57.706 45.455 0.00 0.00 39.88 4.18
2169 3560 2.370849 TGTCAACCTCCTACTGGAAACC 59.629 50.000 0.00 0.00 42.66 3.27
2187 3578 1.442526 CCGATGCTAGCCTTGCCAAG 61.443 60.000 13.29 0.00 0.00 3.61
2199 3590 2.589014 CTTGCCAAGATTGCGAGAAAC 58.411 47.619 0.00 0.00 41.87 2.78
2208 3599 3.441572 AGATTGCGAGAAACAATGGGAAG 59.558 43.478 0.00 0.00 37.85 3.46
2464 3855 5.447279 GGCAATATCGTTGTAAGTGAACAGG 60.447 44.000 0.00 0.00 0.00 4.00
2465 3856 5.560148 CAATATCGTTGTAAGTGAACAGGC 58.440 41.667 0.00 0.00 0.00 4.85
2469 3860 3.880490 TCGTTGTAAGTGAACAGGCATTT 59.120 39.130 0.00 0.00 0.00 2.32
2548 3969 6.014840 CCTGTCCTGTTACTTACTGAACCTAA 60.015 42.308 0.00 0.00 0.00 2.69
2559 3980 7.762382 ACTTACTGAACCTAATTTTGCTATGC 58.238 34.615 0.00 0.00 0.00 3.14
2563 3984 6.543831 ACTGAACCTAATTTTGCTATGCCTAG 59.456 38.462 0.00 0.00 0.00 3.02
2596 4039 6.102663 GCTGTAAACATCTTCTCTGCTTAGA 58.897 40.000 0.00 0.00 0.00 2.10
2599 4042 8.484641 TGTAAACATCTTCTCTGCTTAGAATG 57.515 34.615 2.40 2.49 35.04 2.67
2600 4043 8.097038 TGTAAACATCTTCTCTGCTTAGAATGT 58.903 33.333 2.40 3.00 35.04 2.71
2601 4044 6.981762 AACATCTTCTCTGCTTAGAATGTG 57.018 37.500 7.95 8.84 35.04 3.21
2604 4048 6.762187 ACATCTTCTCTGCTTAGAATGTGATG 59.238 38.462 17.75 17.75 39.36 3.07
2611 4055 7.279536 TCTCTGCTTAGAATGTGATGATGTTTC 59.720 37.037 0.00 0.00 0.00 2.78
2613 4057 7.609146 TCTGCTTAGAATGTGATGATGTTTCTT 59.391 33.333 0.00 0.00 0.00 2.52
2753 4205 8.994429 ACTGATGTCTCTTAGTAATTGTTCTG 57.006 34.615 0.00 0.00 0.00 3.02
2794 4246 6.508777 TCCTATTTTGCAGTGGTTTTTGTAC 58.491 36.000 0.00 0.00 0.00 2.90
2851 4304 4.081642 GTGCAGACCCTACTATCAGTTGAA 60.082 45.833 0.00 0.00 0.00 2.69
2881 4334 3.814625 TGTCAATGCAGTTAACAGGTCA 58.185 40.909 8.61 0.27 0.00 4.02
2930 4383 5.684704 AGAAGATGAACAACCAAGAACTCA 58.315 37.500 0.00 0.00 0.00 3.41
2932 4385 6.774656 AGAAGATGAACAACCAAGAACTCATT 59.225 34.615 0.00 0.00 0.00 2.57
3310 4763 0.391597 TGTTCCTGGTGTTCGACTCC 59.608 55.000 0.00 0.00 32.62 3.85
3397 4850 1.272147 GCCAAGAGGAGGATGGTGTTT 60.272 52.381 0.00 0.00 36.57 2.83
3442 4895 1.522580 GTGCCTCTTCATCTCCGCC 60.523 63.158 0.00 0.00 0.00 6.13
3445 4898 2.279784 CTCTTCATCTCCGCCGCC 60.280 66.667 0.00 0.00 0.00 6.13
3460 4913 4.521075 GCCTTCATAGCGCTGACA 57.479 55.556 22.90 0.00 0.00 3.58
3607 5060 3.779183 AGAGCATGAGGAAGATCAGGAAA 59.221 43.478 0.00 0.00 32.83 3.13
3661 5114 3.808656 GTCGACTCGGACCCGGAC 61.809 72.222 8.70 4.41 40.25 4.79
3777 5231 0.454620 TTTCGCTCGAGTCTCTTCGC 60.455 55.000 15.13 0.00 40.29 4.70
3796 5250 5.890110 TCGCTCGAATGATGAATAACTTC 57.110 39.130 0.00 0.00 0.00 3.01
3857 5311 6.694447 ACTTTTGCTGCTGAAACAATATCAT 58.306 32.000 0.00 0.00 0.00 2.45
3858 5312 6.810182 ACTTTTGCTGCTGAAACAATATCATC 59.190 34.615 0.00 0.00 0.00 2.92
3859 5313 5.900865 TTGCTGCTGAAACAATATCATCA 57.099 34.783 0.00 0.00 0.00 3.07
3978 5432 5.003778 GCTTCTTGTACGCATAATTTTGCAG 59.996 40.000 18.95 13.91 42.91 4.41
3979 5433 5.621197 TCTTGTACGCATAATTTTGCAGT 57.379 34.783 18.95 17.85 42.91 4.40
3989 5443 6.479001 CGCATAATTTTGCAGTAGTACCTACT 59.521 38.462 18.95 0.00 46.75 2.57
4003 5457 9.452287 AGTAGTACCTACTGTTTTTCTAGAGAG 57.548 37.037 3.21 0.00 44.47 3.20
4004 5458 9.230122 GTAGTACCTACTGTTTTTCTAGAGAGT 57.770 37.037 0.00 0.00 37.10 3.24
4006 5460 9.230122 AGTACCTACTGTTTTTCTAGAGAGTAC 57.770 37.037 0.00 0.00 34.72 2.73
4007 5461 7.143514 ACCTACTGTTTTTCTAGAGAGTACG 57.856 40.000 0.00 0.00 0.00 3.67
4008 5462 6.028987 CCTACTGTTTTTCTAGAGAGTACGC 58.971 44.000 0.00 0.00 0.00 4.42
4009 5463 4.807443 ACTGTTTTTCTAGAGAGTACGCC 58.193 43.478 0.00 0.00 0.00 5.68
4010 5464 4.280174 ACTGTTTTTCTAGAGAGTACGCCA 59.720 41.667 0.00 0.00 0.00 5.69
4011 5465 5.204409 TGTTTTTCTAGAGAGTACGCCAA 57.796 39.130 0.00 0.00 0.00 4.52
4012 5466 4.986659 TGTTTTTCTAGAGAGTACGCCAAC 59.013 41.667 0.00 0.00 0.00 3.77
4014 5468 1.376543 TCTAGAGAGTACGCCAACGG 58.623 55.000 0.00 0.00 46.04 4.44
4015 5469 1.093159 CTAGAGAGTACGCCAACGGT 58.907 55.000 0.00 0.00 46.04 4.83
4016 5470 0.806868 TAGAGAGTACGCCAACGGTG 59.193 55.000 0.00 0.00 46.04 4.94
4018 5472 0.523072 GAGAGTACGCCAACGGTGTA 59.477 55.000 0.00 2.32 45.32 2.90
4051 5505 7.923414 TTAGAGAAGGGAGCAAAAGATTTAC 57.077 36.000 0.00 0.00 0.00 2.01
4053 5507 5.942826 AGAGAAGGGAGCAAAAGATTTACAG 59.057 40.000 0.00 0.00 0.00 2.74
4087 5552 6.831769 ACATTCGACAAAGATAACATCACAC 58.168 36.000 0.00 0.00 0.00 3.82
4101 5566 1.214217 TCACACCCACACCTACCAAA 58.786 50.000 0.00 0.00 0.00 3.28
4104 5569 1.567175 ACACCCACACCTACCAAAGTT 59.433 47.619 0.00 0.00 0.00 2.66
4109 5574 4.070009 CCCACACCTACCAAAGTTCTAAC 58.930 47.826 0.00 0.00 0.00 2.34
4118 5583 7.039853 ACCTACCAAAGTTCTAACACTACTCTC 60.040 40.741 0.00 0.00 0.00 3.20
4127 5592 9.298250 AGTTCTAACACTACTCTCTCACAAATA 57.702 33.333 0.00 0.00 0.00 1.40
4165 5630 5.647658 CACACCACCTATAGCAATCTTTCAA 59.352 40.000 0.00 0.00 0.00 2.69
4178 5643 5.585390 CAATCTTTCAATCCCTCAATTCCG 58.415 41.667 0.00 0.00 0.00 4.30
4205 5670 1.510480 GGCACTGCACAGTTGACTCC 61.510 60.000 0.00 0.00 40.20 3.85
4223 5688 1.065401 TCCGCTGTTTTTGTTGCTGAG 59.935 47.619 0.00 0.00 0.00 3.35
4229 5694 4.735338 GCTGTTTTTGTTGCTGAGTTCTAC 59.265 41.667 0.00 0.00 0.00 2.59
4230 5695 5.243426 TGTTTTTGTTGCTGAGTTCTACC 57.757 39.130 0.00 0.00 0.00 3.18
4244 5709 0.325296 TCTACCGAAGACCCTGGCAT 60.325 55.000 0.00 0.00 0.00 4.40
4259 5724 0.750911 GGCATTCCTCTGCTTCCAGG 60.751 60.000 0.00 0.00 41.95 4.45
4300 5765 2.659897 ATCGCATCGAAGCCTCGC 60.660 61.111 7.11 0.00 45.04 5.03
4332 5797 2.146342 CCTGAAGAGCTTTCTTTGCGA 58.854 47.619 9.17 0.00 35.28 5.10
4335 5800 2.545526 TGAAGAGCTTTCTTTGCGACAG 59.454 45.455 9.17 0.00 35.28 3.51
4340 5805 0.040067 CTTTCTTTGCGACAGCCACC 60.040 55.000 0.00 0.00 44.33 4.61
4352 5817 1.077663 ACAGCCACCAATCCAGGAAAT 59.922 47.619 0.00 0.00 0.00 2.17
4367 5832 6.588719 CCAGGAAATGGTCATTTTTACTCA 57.411 37.500 9.88 0.00 44.91 3.41
4394 5859 1.224075 CACATTCAGCCGCATAGAGG 58.776 55.000 0.00 0.00 0.00 3.69
4427 5892 2.289382 TGCCAAACTTCTCGAGCATACA 60.289 45.455 7.81 0.00 0.00 2.29
4430 5895 3.123621 CCAAACTTCTCGAGCATACACAC 59.876 47.826 7.81 0.00 0.00 3.82
4434 5899 3.756963 ACTTCTCGAGCATACACACACTA 59.243 43.478 7.81 0.00 0.00 2.74
4438 5903 4.217767 TCTCGAGCATACACACACTAAAGT 59.782 41.667 7.81 0.00 0.00 2.66
4444 5909 7.688167 CGAGCATACACACACTAAAGTAAAATG 59.312 37.037 0.00 0.00 0.00 2.32
4449 5914 7.023197 ACACACACTAAAGTAAAATGTGGTC 57.977 36.000 14.97 0.00 43.94 4.02
4461 5926 0.038166 ATGTGGTCGGCATTGTCCTT 59.962 50.000 0.00 0.00 0.00 3.36
4464 5929 1.066430 GTGGTCGGCATTGTCCTTCTA 60.066 52.381 0.00 0.00 0.00 2.10
4501 5966 0.807496 GTGAGTCTTGAAGGCCATGC 59.193 55.000 5.01 0.00 0.00 4.06
4534 6000 6.984474 TCGGTCAGAAGTCCAAATTGTATATC 59.016 38.462 0.00 0.00 0.00 1.63
4535 6001 6.202954 CGGTCAGAAGTCCAAATTGTATATCC 59.797 42.308 0.00 0.00 0.00 2.59
4537 6003 8.429641 GGTCAGAAGTCCAAATTGTATATCCTA 58.570 37.037 0.00 0.00 0.00 2.94
4544 6010 6.428159 GTCCAAATTGTATATCCTACTGCCAG 59.572 42.308 0.00 0.00 0.00 4.85
4561 6027 2.931320 GCCAGCTGCTACTCGTAAACTT 60.931 50.000 8.66 0.00 36.87 2.66
4577 6043 6.492087 TCGTAAACTTCATTGGGATTTTTCCT 59.508 34.615 0.00 0.00 0.00 3.36
4578 6044 6.806739 CGTAAACTTCATTGGGATTTTTCCTC 59.193 38.462 0.00 0.00 0.00 3.71
4579 6045 6.745794 AAACTTCATTGGGATTTTTCCTCA 57.254 33.333 0.00 0.00 0.00 3.86
4660 6126 7.461918 GTTTATCGAACCAATAGAAGAACCAC 58.538 38.462 0.00 0.00 31.85 4.16
4661 6127 4.610605 TCGAACCAATAGAAGAACCACA 57.389 40.909 0.00 0.00 0.00 4.17
4671 6137 6.727824 ATAGAAGAACCACACAAATTCTCG 57.272 37.500 0.00 0.00 31.44 4.04
4676 6142 4.511826 AGAACCACACAAATTCTCGTCTTC 59.488 41.667 0.00 0.00 0.00 2.87
4677 6143 2.800544 ACCACACAAATTCTCGTCTTCG 59.199 45.455 0.00 0.00 38.55 3.79
4685 6151 1.471119 TTCTCGTCTTCGGCACCTAT 58.529 50.000 0.00 0.00 37.69 2.57
4686 6152 2.336945 TCTCGTCTTCGGCACCTATA 57.663 50.000 0.00 0.00 37.69 1.31
4695 6161 2.967362 TCGGCACCTATACACACAAAG 58.033 47.619 0.00 0.00 0.00 2.77
4696 6162 1.396996 CGGCACCTATACACACAAAGC 59.603 52.381 0.00 0.00 0.00 3.51
4700 6166 4.082245 GGCACCTATACACACAAAGCAAAT 60.082 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.167691 ACTGATTTATCTGGCAGGGATTATAT 57.832 34.615 15.73 1.01 32.82 0.86
24 25 6.460103 ACTGATTTATCTGGCAGGGATTAT 57.540 37.500 15.73 2.57 32.82 1.28
31 32 5.122239 TCGTTCAAACTGATTTATCTGGCAG 59.878 40.000 8.58 8.58 34.65 4.85
32 33 5.000591 TCGTTCAAACTGATTTATCTGGCA 58.999 37.500 0.00 0.00 0.00 4.92
71 72 7.717875 GGTAAGGTATTGTGTAATATTGCCTCA 59.282 37.037 0.00 0.00 31.81 3.86
120 1463 6.500041 GCTCCCACTAGCTCGATAATAATAG 58.500 44.000 0.00 0.00 39.50 1.73
224 1572 4.058124 GGTTGGTTTCTTGAATTTCCAGC 58.942 43.478 0.00 0.00 0.00 4.85
265 1613 0.892358 CTCTGCTTGGCCTCTTTGCA 60.892 55.000 3.32 6.42 0.00 4.08
354 1703 0.983378 CGGGAATCTTGGACCTCCCT 60.983 60.000 12.70 0.00 44.75 4.20
356 1705 1.153147 GCGGGAATCTTGGACCTCC 60.153 63.158 0.00 0.00 0.00 4.30
510 1866 0.684535 ACCAATTTCGCCCCAAAAGG 59.315 50.000 0.00 0.00 0.00 3.11
542 1898 5.515106 TGAGACAGGAGAAAAAGGGAAAAA 58.485 37.500 0.00 0.00 0.00 1.94
546 1902 3.318313 ACTGAGACAGGAGAAAAAGGGA 58.682 45.455 0.00 0.00 35.51 4.20
651 2016 0.463295 ATCTCAGCATTCGTGCCAGG 60.463 55.000 0.00 0.00 34.90 4.45
656 2021 1.741706 AGGCAAATCTCAGCATTCGTG 59.258 47.619 0.00 0.00 0.00 4.35
702 2067 1.570857 TACCCCTGGGCCATGAACAG 61.571 60.000 6.72 1.32 39.32 3.16
716 2081 2.838637 TCCCAACCAATCAATACCCC 57.161 50.000 0.00 0.00 0.00 4.95
731 2096 4.802051 GCAAGCGCTGGGATCCCA 62.802 66.667 31.83 31.83 45.02 4.37
771 2136 1.205655 TCTCTGATTGACGGGAAGCAG 59.794 52.381 7.42 7.42 40.10 4.24
782 2149 3.439476 CCAAGACTTGCCTTCTCTGATTG 59.561 47.826 9.85 0.00 0.00 2.67
811 2179 1.202580 GGACCTGAGATTGTGATCGGG 60.203 57.143 0.00 0.00 45.88 5.14
812 2180 1.202580 GGGACCTGAGATTGTGATCGG 60.203 57.143 0.00 0.00 37.37 4.18
836 2204 0.906775 AGCCCCCTGATTTGCAATTG 59.093 50.000 0.00 0.00 0.00 2.32
860 2228 9.739276 TTGCTTCTCTTGATTAGATTAGGAAAA 57.261 29.630 0.00 0.00 30.92 2.29
862 2230 7.770897 GGTTGCTTCTCTTGATTAGATTAGGAA 59.229 37.037 0.00 0.00 30.92 3.36
863 2231 7.275920 GGTTGCTTCTCTTGATTAGATTAGGA 58.724 38.462 0.00 0.00 30.92 2.94
864 2232 6.201806 CGGTTGCTTCTCTTGATTAGATTAGG 59.798 42.308 0.00 0.00 30.92 2.69
865 2233 6.758886 ACGGTTGCTTCTCTTGATTAGATTAG 59.241 38.462 0.00 0.00 30.92 1.73
866 2234 6.640518 ACGGTTGCTTCTCTTGATTAGATTA 58.359 36.000 0.00 0.00 30.92 1.75
867 2235 5.491982 ACGGTTGCTTCTCTTGATTAGATT 58.508 37.500 0.00 0.00 30.92 2.40
868 2236 5.091261 ACGGTTGCTTCTCTTGATTAGAT 57.909 39.130 0.00 0.00 30.92 1.98
869 2237 4.537135 ACGGTTGCTTCTCTTGATTAGA 57.463 40.909 0.00 0.00 0.00 2.10
870 2238 6.291849 CGATTACGGTTGCTTCTCTTGATTAG 60.292 42.308 0.00 0.00 35.72 1.73
871 2239 5.518847 CGATTACGGTTGCTTCTCTTGATTA 59.481 40.000 0.00 0.00 35.72 1.75
921 2303 2.095059 CCTGTTCTTGCGAAAATCCAGG 60.095 50.000 1.40 1.40 35.01 4.45
922 2304 2.095059 CCCTGTTCTTGCGAAAATCCAG 60.095 50.000 0.00 0.00 0.00 3.86
923 2305 1.885887 CCCTGTTCTTGCGAAAATCCA 59.114 47.619 0.00 0.00 0.00 3.41
924 2306 1.202348 CCCCTGTTCTTGCGAAAATCC 59.798 52.381 0.00 0.00 0.00 3.01
925 2307 1.402852 GCCCCTGTTCTTGCGAAAATC 60.403 52.381 0.00 0.00 0.00 2.17
926 2308 0.603065 GCCCCTGTTCTTGCGAAAAT 59.397 50.000 0.00 0.00 0.00 1.82
927 2309 2.037871 GCCCCTGTTCTTGCGAAAA 58.962 52.632 0.00 0.00 0.00 2.29
928 2310 3.758172 GCCCCTGTTCTTGCGAAA 58.242 55.556 0.00 0.00 0.00 3.46
932 2314 0.887387 TGTAACGCCCCTGTTCTTGC 60.887 55.000 0.00 0.00 33.32 4.01
933 2315 1.600023 TTGTAACGCCCCTGTTCTTG 58.400 50.000 0.00 0.00 33.32 3.02
934 2316 2.351706 TTTGTAACGCCCCTGTTCTT 57.648 45.000 0.00 0.00 33.32 2.52
996 2378 0.545071 TGGTCTGCCTCTCCATGTCA 60.545 55.000 0.00 0.00 35.27 3.58
1065 2447 2.358247 TTGCTCCGCCGGAAGTTC 60.358 61.111 7.50 0.00 0.00 3.01
1382 2764 3.347216 ACAATATGCTGGACTGGTGAAC 58.653 45.455 0.00 0.00 0.00 3.18
1383 2765 3.719268 ACAATATGCTGGACTGGTGAA 57.281 42.857 0.00 0.00 0.00 3.18
1447 2830 6.624423 CCCAAATCCTGATTACAAAGACTTG 58.376 40.000 0.00 0.00 38.61 3.16
1484 2867 1.585668 CGAAGCAATCTACTCACTGCG 59.414 52.381 0.00 0.00 39.80 5.18
1518 2904 7.443575 CCACCAACTCAATCAGATAAGAATAGG 59.556 40.741 0.70 0.00 0.00 2.57
1544 2930 5.250235 TCTTGCTGTGAGTACTACTATGC 57.750 43.478 0.00 0.00 0.00 3.14
1551 2937 3.384789 TCACTGTTCTTGCTGTGAGTACT 59.615 43.478 0.00 0.00 40.63 2.73
1554 2940 2.988010 TCACTGTTCTTGCTGTGAGT 57.012 45.000 0.00 0.00 40.63 3.41
1584 2970 8.401490 AGCACTTGTTCTTAGATGAAAAGATT 57.599 30.769 0.00 0.00 33.17 2.40
1690 3077 4.568072 TGTCAGTTGCCACCTACATAAT 57.432 40.909 0.00 0.00 0.00 1.28
1691 3078 4.202419 ACTTGTCAGTTGCCACCTACATAA 60.202 41.667 0.00 0.00 0.00 1.90
1692 3079 3.326588 ACTTGTCAGTTGCCACCTACATA 59.673 43.478 0.00 0.00 0.00 2.29
1743 3130 6.432472 CAGAATTTCCCTAGCCCTCATAAATC 59.568 42.308 0.00 0.00 0.00 2.17
1991 3382 7.910584 AGAATAAGCCACAATTCTTTTGGAAT 58.089 30.769 0.00 0.00 45.61 3.01
2169 3560 0.462581 TCTTGGCAAGGCTAGCATCG 60.463 55.000 25.92 0.00 0.00 3.84
2187 3578 3.440173 TCTTCCCATTGTTTCTCGCAATC 59.560 43.478 0.00 0.00 34.68 2.67
2199 3590 3.731652 TGCAAAACTGTCTTCCCATTG 57.268 42.857 0.00 0.00 0.00 2.82
2208 3599 0.729140 CCGCGGAATGCAAAACTGTC 60.729 55.000 24.07 0.00 46.97 3.51
2493 3884 9.851686 ACAGGATAGCAAATGATTGATAAACTA 57.148 29.630 0.00 0.00 40.49 2.24
2494 3885 8.627403 CACAGGATAGCAAATGATTGATAAACT 58.373 33.333 0.00 0.00 40.49 2.66
2729 4178 8.994429 ACAGAACAATTACTAAGAGACATCAG 57.006 34.615 0.00 0.00 0.00 2.90
2753 4205 7.511959 AAATAGGAACTGGAAAGTTCTCAAC 57.488 36.000 15.94 2.57 45.34 3.18
2794 4246 7.050377 AGGAATTACACATGTATCAGTCAAGG 58.950 38.462 0.00 0.00 0.00 3.61
2836 4289 6.485830 TCAATCCCTTCAACTGATAGTAGG 57.514 41.667 0.00 0.00 0.00 3.18
2851 4304 3.377253 ACTGCATTGACATCAATCCCT 57.623 42.857 4.08 0.00 44.10 4.20
2930 4383 3.448686 CGGCGTCTCTCAGAATGTTAAT 58.551 45.455 0.00 0.00 37.40 1.40
2932 4385 1.134367 CCGGCGTCTCTCAGAATGTTA 59.866 52.381 6.01 0.00 37.40 2.41
2959 4412 0.521735 CCGGCTCTTTTGCAGTTACC 59.478 55.000 0.00 0.00 34.04 2.85
3310 4763 1.591059 CGAGATGAAGAGCGCCAGG 60.591 63.158 2.29 0.00 0.00 4.45
3397 4850 2.815503 CCACATGAGCTTGTTCATCACA 59.184 45.455 0.00 0.00 35.67 3.58
3445 4898 2.721603 GACGTATGTCAGCGCTATGAAG 59.278 50.000 10.99 0.00 44.82 3.02
3460 4913 4.183686 CGGCCGACCACGACGTAT 62.184 66.667 24.07 0.00 42.66 3.06
3661 5114 3.056821 TCTTGTACTCGGTGTTGATCAGG 60.057 47.826 0.00 0.00 0.00 3.86
3796 5250 3.133721 TCAAAATGTCAAAACCCCACTGG 59.866 43.478 0.00 0.00 41.37 4.00
3857 5311 1.047801 TACAAGCACAGCTGAGGTGA 58.952 50.000 23.35 4.74 39.62 4.02
3858 5312 2.105006 ATACAAGCACAGCTGAGGTG 57.895 50.000 23.35 10.51 39.62 4.00
3859 5313 2.430465 CAATACAAGCACAGCTGAGGT 58.570 47.619 23.35 16.38 39.62 3.85
3989 5443 4.859304 TGGCGTACTCTCTAGAAAAACA 57.141 40.909 0.00 0.00 0.00 2.83
3991 5445 4.232221 CGTTGGCGTACTCTCTAGAAAAA 58.768 43.478 0.00 0.00 0.00 1.94
3992 5446 3.366679 CCGTTGGCGTACTCTCTAGAAAA 60.367 47.826 0.00 0.00 36.15 2.29
3993 5447 2.163010 CCGTTGGCGTACTCTCTAGAAA 59.837 50.000 0.00 0.00 36.15 2.52
3994 5448 1.741706 CCGTTGGCGTACTCTCTAGAA 59.258 52.381 0.00 0.00 36.15 2.10
3995 5449 1.339438 ACCGTTGGCGTACTCTCTAGA 60.339 52.381 0.00 0.00 36.15 2.43
3996 5450 1.093159 ACCGTTGGCGTACTCTCTAG 58.907 55.000 0.00 0.00 36.15 2.43
3997 5451 0.806868 CACCGTTGGCGTACTCTCTA 59.193 55.000 0.00 0.00 36.15 2.43
3998 5452 1.177256 ACACCGTTGGCGTACTCTCT 61.177 55.000 0.00 0.00 36.15 3.10
3999 5453 0.523072 TACACCGTTGGCGTACTCTC 59.477 55.000 0.00 0.00 36.15 3.20
4000 5454 1.133790 GATACACCGTTGGCGTACTCT 59.866 52.381 0.00 0.00 36.15 3.24
4001 5455 1.135315 TGATACACCGTTGGCGTACTC 60.135 52.381 0.00 0.00 36.15 2.59
4002 5456 0.889994 TGATACACCGTTGGCGTACT 59.110 50.000 0.00 0.00 36.15 2.73
4003 5457 1.930567 ATGATACACCGTTGGCGTAC 58.069 50.000 0.00 0.00 36.15 3.67
4004 5458 4.325028 AATATGATACACCGTTGGCGTA 57.675 40.909 0.00 0.00 36.15 4.42
4005 5459 2.902705 ATATGATACACCGTTGGCGT 57.097 45.000 0.00 0.00 36.15 5.68
4006 5460 4.545823 AAAATATGATACACCGTTGGCG 57.454 40.909 0.00 0.00 37.95 5.69
4007 5461 7.225931 TCTCTAAAAATATGATACACCGTTGGC 59.774 37.037 0.00 0.00 0.00 4.52
4008 5462 8.657074 TCTCTAAAAATATGATACACCGTTGG 57.343 34.615 0.00 0.00 0.00 3.77
4010 5464 9.326413 CCTTCTCTAAAAATATGATACACCGTT 57.674 33.333 0.00 0.00 0.00 4.44
4011 5465 7.931948 CCCTTCTCTAAAAATATGATACACCGT 59.068 37.037 0.00 0.00 0.00 4.83
4012 5466 8.148351 TCCCTTCTCTAAAAATATGATACACCG 58.852 37.037 0.00 0.00 0.00 4.94
4013 5467 9.495572 CTCCCTTCTCTAAAAATATGATACACC 57.504 37.037 0.00 0.00 0.00 4.16
4014 5468 8.994170 GCTCCCTTCTCTAAAAATATGATACAC 58.006 37.037 0.00 0.00 0.00 2.90
4015 5469 8.713971 TGCTCCCTTCTCTAAAAATATGATACA 58.286 33.333 0.00 0.00 0.00 2.29
4016 5470 9.561069 TTGCTCCCTTCTCTAAAAATATGATAC 57.439 33.333 0.00 0.00 0.00 2.24
4018 5472 9.479549 TTTTGCTCCCTTCTCTAAAAATATGAT 57.520 29.630 0.00 0.00 0.00 2.45
4019 5473 8.877864 TTTTGCTCCCTTCTCTAAAAATATGA 57.122 30.769 0.00 0.00 0.00 2.15
4020 5474 8.960591 TCTTTTGCTCCCTTCTCTAAAAATATG 58.039 33.333 0.00 0.00 0.00 1.78
4021 5475 9.706529 ATCTTTTGCTCCCTTCTCTAAAAATAT 57.293 29.630 0.00 0.00 0.00 1.28
4022 5476 9.533831 AATCTTTTGCTCCCTTCTCTAAAAATA 57.466 29.630 0.00 0.00 0.00 1.40
4023 5477 8.427902 AATCTTTTGCTCCCTTCTCTAAAAAT 57.572 30.769 0.00 0.00 0.00 1.82
4082 5547 1.142060 CTTTGGTAGGTGTGGGTGTGA 59.858 52.381 0.00 0.00 0.00 3.58
4083 5548 1.133915 ACTTTGGTAGGTGTGGGTGTG 60.134 52.381 0.00 0.00 0.00 3.82
4087 5552 2.951229 AGAACTTTGGTAGGTGTGGG 57.049 50.000 0.00 0.00 0.00 4.61
4101 5566 7.584122 TTTGTGAGAGAGTAGTGTTAGAACT 57.416 36.000 0.00 0.00 0.00 3.01
4104 5569 9.688091 AGATATTTGTGAGAGAGTAGTGTTAGA 57.312 33.333 0.00 0.00 0.00 2.10
4109 5574 9.645059 TTTCAAGATATTTGTGAGAGAGTAGTG 57.355 33.333 0.00 0.00 0.00 2.74
4118 5583 7.094248 TGTGGATGGTTTCAAGATATTTGTGAG 60.094 37.037 0.00 0.00 0.00 3.51
4127 5592 3.157087 GTGGTGTGGATGGTTTCAAGAT 58.843 45.455 0.00 0.00 0.00 2.40
4165 5630 4.718961 CCATCTTAACGGAATTGAGGGAT 58.281 43.478 0.00 0.00 31.14 3.85
4178 5643 2.154462 ACTGTGCAGTGCCATCTTAAC 58.846 47.619 13.72 2.35 40.75 2.01
4205 5670 2.193306 ACTCAGCAACAAAAACAGCG 57.807 45.000 0.00 0.00 0.00 5.18
4223 5688 0.108281 GCCAGGGTCTTCGGTAGAAC 60.108 60.000 0.00 0.00 40.06 3.01
4229 5694 1.452108 GGAATGCCAGGGTCTTCGG 60.452 63.158 0.00 0.00 0.00 4.30
4230 5695 0.462759 GAGGAATGCCAGGGTCTTCG 60.463 60.000 0.00 0.00 36.29 3.79
4244 5709 0.117140 TCTCCCTGGAAGCAGAGGAA 59.883 55.000 0.00 0.00 34.62 3.36
4259 5724 2.527951 ATCGCAGTTGCCTGGTCTCC 62.528 60.000 0.00 0.00 39.22 3.71
4265 5730 1.028330 ATGGTGATCGCAGTTGCCTG 61.028 55.000 8.82 0.00 41.91 4.85
4300 5765 2.615869 CTCTTCAGGGCGAAAGAGAAG 58.384 52.381 13.72 0.00 37.60 2.85
4309 5774 1.198637 CAAAGAAAGCTCTTCAGGGCG 59.801 52.381 10.08 0.00 41.23 6.13
4332 5797 0.482446 TTTCCTGGATTGGTGGCTGT 59.518 50.000 0.00 0.00 0.00 4.40
4352 5817 4.321899 GCAATGCCTGAGTAAAAATGACCA 60.322 41.667 0.00 0.00 0.00 4.02
4354 5819 4.622740 GTGCAATGCCTGAGTAAAAATGAC 59.377 41.667 1.53 0.00 0.00 3.06
4361 5826 3.419943 TGAATGTGCAATGCCTGAGTAA 58.580 40.909 1.53 0.00 0.00 2.24
4367 5832 1.895238 GGCTGAATGTGCAATGCCT 59.105 52.632 1.53 0.00 37.58 4.75
4414 5879 4.776795 TTAGTGTGTGTATGCTCGAGAA 57.223 40.909 18.75 5.90 0.00 2.87
4427 5892 5.237779 CCGACCACATTTTACTTTAGTGTGT 59.762 40.000 0.00 0.00 38.72 3.72
4430 5895 4.214545 TGCCGACCACATTTTACTTTAGTG 59.785 41.667 0.00 0.00 0.00 2.74
4434 5899 4.038642 ACAATGCCGACCACATTTTACTTT 59.961 37.500 0.00 0.00 35.58 2.66
4438 5903 2.490115 GGACAATGCCGACCACATTTTA 59.510 45.455 0.00 0.00 35.58 1.52
4444 5909 0.321653 AGAAGGACAATGCCGACCAC 60.322 55.000 0.00 0.00 0.00 4.16
4449 5914 4.542662 CTTCAATAGAAGGACAATGCCG 57.457 45.455 0.00 0.00 46.01 5.69
4461 5926 7.093333 ACTCACCATACACATGTCTTCAATAGA 60.093 37.037 0.00 0.00 0.00 1.98
4464 5929 5.809001 ACTCACCATACACATGTCTTCAAT 58.191 37.500 0.00 0.00 0.00 2.57
4471 5936 4.890158 TCAAGACTCACCATACACATGT 57.110 40.909 0.00 0.00 0.00 3.21
4516 5982 7.173390 GGCAGTAGGATATACAATTTGGACTTC 59.827 40.741 0.78 0.00 0.00 3.01
4544 6010 4.201724 CCAATGAAGTTTACGAGTAGCAGC 60.202 45.833 0.00 0.00 0.00 5.25
4561 6027 4.095946 CCCTTGAGGAAAAATCCCAATGA 58.904 43.478 0.00 0.00 38.24 2.57
4577 6043 1.065410 TGCTTCACCCTTCCCCTTGA 61.065 55.000 0.00 0.00 0.00 3.02
4578 6044 0.610232 CTGCTTCACCCTTCCCCTTG 60.610 60.000 0.00 0.00 0.00 3.61
4579 6045 1.068352 ACTGCTTCACCCTTCCCCTT 61.068 55.000 0.00 0.00 0.00 3.95
4618 6084 5.163509 CGATAAACCTGATTCTCACTGAGGA 60.164 44.000 6.20 0.00 0.00 3.71
4622 6088 6.337853 GTTCGATAAACCTGATTCTCACTG 57.662 41.667 0.00 0.00 31.20 3.66
4636 6102 7.118680 GTGTGGTTCTTCTATTGGTTCGATAAA 59.881 37.037 0.00 0.00 0.00 1.40
4642 6108 6.385649 TTTGTGTGGTTCTTCTATTGGTTC 57.614 37.500 0.00 0.00 0.00 3.62
4646 6112 7.017645 CGAGAATTTGTGTGGTTCTTCTATTG 58.982 38.462 0.00 0.00 32.67 1.90
4652 6118 4.451900 AGACGAGAATTTGTGTGGTTCTT 58.548 39.130 0.00 0.00 32.67 2.52
4660 6126 1.798223 TGCCGAAGACGAGAATTTGTG 59.202 47.619 0.00 0.00 42.66 3.33
4661 6127 1.798813 GTGCCGAAGACGAGAATTTGT 59.201 47.619 0.00 0.00 42.66 2.83
4671 6137 2.094390 TGTGTGTATAGGTGCCGAAGAC 60.094 50.000 0.00 0.00 0.00 3.01
4676 6142 1.396996 GCTTTGTGTGTATAGGTGCCG 59.603 52.381 0.00 0.00 0.00 5.69
4677 6143 2.432444 TGCTTTGTGTGTATAGGTGCC 58.568 47.619 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.