Multiple sequence alignment - TraesCS2D01G239300

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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 TraesCS2D01G239300 chr2D 100.000 5375 0 0 1 5375 252146187 252140813 0.000000e+00 9926.0
1 TraesCS2D01G239300 chr2D 96.429 56 1 1 4885 4939 22175437 22175382 2.060000e-14 91.6
2 TraesCS2D01G239300 chr2D 95.238 42 2 0 1327 1368 100188203 100188244 3.470000e-07 67.6
3 TraesCS2D01G239300 chr2A 96.634 2555 55 4 1998 4533 234290293 234287751 0.000000e+00 4213.0
4 TraesCS2D01G239300 chr2A 92.828 1241 42 20 760 1972 234291510 234290289 0.000000e+00 1755.0
5 TraesCS2D01G239300 chr2A 92.789 735 49 4 1 734 234292235 234291504 0.000000e+00 1061.0
6 TraesCS2D01G239300 chr2A 98.658 447 5 1 4929 5375 278992042 278992487 0.000000e+00 791.0
7 TraesCS2D01G239300 chr2A 89.005 573 55 4 6 577 426718945 426718380 0.000000e+00 702.0
8 TraesCS2D01G239300 chr2A 96.154 338 13 0 4542 4879 278991703 278992040 2.190000e-153 553.0
9 TraesCS2D01G239300 chr2B 91.739 1610 48 13 3271 4863 278810710 278809169 0.000000e+00 2158.0
10 TraesCS2D01G239300 chr2B 94.010 1035 33 5 1856 2868 278821468 278820441 0.000000e+00 1541.0
11 TraesCS2D01G239300 chr2B 97.511 442 11 0 4934 5375 278809175 278808734 0.000000e+00 756.0
12 TraesCS2D01G239300 chr2B 89.691 582 29 20 816 1375 278908178 278907606 0.000000e+00 713.0
13 TraesCS2D01G239300 chr2B 92.901 493 25 7 1373 1859 278907568 278907080 0.000000e+00 708.0
14 TraesCS2D01G239300 chr2B 94.595 407 13 1 2877 3274 278814926 278814520 5.910000e-174 621.0
15 TraesCS2D01G239300 chr2B 94.737 57 2 1 4880 4935 644171865 644171921 2.670000e-13 87.9
16 TraesCS2D01G239300 chr2B 88.406 69 6 2 4880 4946 250267278 250267210 1.240000e-11 82.4
17 TraesCS2D01G239300 chr2B 97.674 43 1 0 1323 1365 76914671 76914713 2.080000e-09 75.0
18 TraesCS2D01G239300 chr5A 89.737 799 74 7 6 803 649864883 649864092 0.000000e+00 1014.0
19 TraesCS2D01G239300 chr5A 87.156 218 24 4 1462 1678 631862034 631862248 1.500000e-60 244.0
20 TraesCS2D01G239300 chr5A 91.549 71 6 0 1604 1674 671164007 671163937 1.230000e-16 99.0
21 TraesCS2D01G239300 chr5A 98.113 53 0 1 4880 4932 313907691 313907742 2.060000e-14 91.6
22 TraesCS2D01G239300 chr3D 85.193 493 59 11 307 792 490307132 490306647 1.340000e-135 494.0
23 TraesCS2D01G239300 chr7B 87.607 234 26 2 1456 1687 511960062 511960294 8.870000e-68 268.0
24 TraesCS2D01G239300 chr7B 94.915 59 1 2 4880 4937 611935209 611935266 2.060000e-14 91.6
25 TraesCS2D01G239300 chr7B 94.737 57 3 0 4881 4937 156633896 156633840 7.410000e-14 89.8
26 TraesCS2D01G239300 chr7B 89.062 64 5 1 736 799 665373569 665373630 1.610000e-10 78.7
27 TraesCS2D01G239300 chr1B 87.671 219 27 0 1460 1678 647533909 647533691 6.910000e-64 255.0
28 TraesCS2D01G239300 chr3B 90.419 167 16 0 1452 1618 493121626 493121792 2.520000e-53 220.0
29 TraesCS2D01G239300 chr3B 89.881 168 15 2 1461 1626 102978558 102978391 1.170000e-51 215.0
30 TraesCS2D01G239300 chr6B 91.720 157 13 0 1462 1618 352091544 352091700 9.060000e-53 219.0
31 TraesCS2D01G239300 chr4A 91.720 157 13 0 1462 1618 674523394 674523550 9.060000e-53 219.0
32 TraesCS2D01G239300 chr4D 87.805 164 19 1 1453 1615 394301843 394302006 1.980000e-44 191.0
33 TraesCS2D01G239300 chr6D 79.365 252 31 7 1456 1688 65495817 65495568 2.000000e-34 158.0
34 TraesCS2D01G239300 chr1D 78.906 256 24 12 1457 1687 411027269 411027019 4.340000e-31 147.0
35 TraesCS2D01G239300 chr1D 91.304 46 4 0 1323 1368 229310824 229310869 4.490000e-06 63.9
36 TraesCS2D01G239300 chr5D 94.828 58 2 1 4879 4936 10367287 10367231 7.410000e-14 89.8
37 TraesCS2D01G239300 chr6A 94.737 57 2 1 4879 4935 4628297 4628242 2.670000e-13 87.9
38 TraesCS2D01G239300 chr1A 82.075 106 16 3 4647 4750 96455737 96455841 2.670000e-13 87.9
39 TraesCS2D01G239300 chr7A 89.394 66 5 2 4880 4944 30721125 30721189 1.240000e-11 82.4
40 TraesCS2D01G239300 chr7A 93.478 46 2 1 1324 1368 611964849 611964804 3.470000e-07 67.6
41 TraesCS2D01G239300 chr5B 97.619 42 1 0 1327 1368 383538846 383538805 7.470000e-09 73.1
42 TraesCS2D01G239300 chr3A 93.333 45 3 0 1324 1368 576272415 576272371 3.470000e-07 67.6
43 TraesCS2D01G239300 chr7D 91.489 47 3 1 1323 1368 550684481 550684435 4.490000e-06 63.9


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 TraesCS2D01G239300 chr2D 252140813 252146187 5374 True 9926.000000 9926 100.000000 1 5375 1 chr2D.!!$R2 5374
1 TraesCS2D01G239300 chr2A 234287751 234292235 4484 True 2343.000000 4213 94.083667 1 4533 3 chr2A.!!$R2 4532
2 TraesCS2D01G239300 chr2A 426718380 426718945 565 True 702.000000 702 89.005000 6 577 1 chr2A.!!$R1 571
3 TraesCS2D01G239300 chr2A 278991703 278992487 784 False 672.000000 791 97.406000 4542 5375 2 chr2A.!!$F1 833
4 TraesCS2D01G239300 chr2B 278820441 278821468 1027 True 1541.000000 1541 94.010000 1856 2868 1 chr2B.!!$R2 1012
5 TraesCS2D01G239300 chr2B 278808734 278814926 6192 True 1178.333333 2158 94.615000 2877 5375 3 chr2B.!!$R3 2498
6 TraesCS2D01G239300 chr2B 278907080 278908178 1098 True 710.500000 713 91.296000 816 1859 2 chr2B.!!$R4 1043
7 TraesCS2D01G239300 chr5A 649864092 649864883 791 True 1014.000000 1014 89.737000 6 803 1 chr5A.!!$R1 797

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
721 723 0.099436 GCCGTCATGTTTGGATCAGC 59.901 55.000 0.00 0.0 0.00 4.26 F
793 795 0.171231 GCTTGGCGAGATTTTGTCCC 59.829 55.000 5.76 0.0 0.00 4.46 F
1062 1091 0.245539 CCGCTCCGTTTAGGTTCTGA 59.754 55.000 0.00 0.0 41.99 3.27 F
1209 1238 0.894835 TCCTGATCTACGTTGCTGCA 59.105 50.000 0.00 0.0 0.00 4.41 F
2937 3036 1.387756 CACCGTCGACCATTAACGAAC 59.612 52.381 10.58 0.0 40.12 3.95 F
4048 7981 3.118075 TCCCACAAAATCCAGCGATATGA 60.118 43.478 0.00 0.0 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1651 0.240945 GACATGGCAACTTTGTCCCG 59.759 55.000 7.56 0.0 41.58 5.14 R
2124 2200 1.645710 ACTGATCCACCCGAGAACTT 58.354 50.000 0.00 0.0 0.00 2.66 R
2267 2364 3.370978 CGTGATGACGCTTTACATTCCTT 59.629 43.478 0.00 0.0 39.10 3.36 R
3069 3168 1.647629 CGCTGGCATCATTCTCTGC 59.352 57.895 0.00 0.0 37.66 4.26 R
4201 8134 0.907486 TGCAGGAGGAGGATGAGTTG 59.093 55.000 0.00 0.0 0.00 3.16 R
5237 9204 1.202533 ACCATGAGCCGACCTAATTCG 60.203 52.381 0.00 0.0 38.80 3.34 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
84 85 6.964807 AAGAATGGCTGTTTATGATGCATA 57.035 33.333 0.00 0.00 0.00 3.14
168 169 1.492176 GGAGGAAGGCAATCCATGAGA 59.508 52.381 11.34 0.00 42.27 3.27
177 178 5.516984 AGGCAATCCATGAGAAAATCTTCT 58.483 37.500 0.00 0.00 38.64 2.85
221 222 4.825085 TGTTTTATCGGTTCTTTTCTGGCT 59.175 37.500 0.00 0.00 0.00 4.75
241 242 3.242543 GCTGACATCTCGGCATTAACAAG 60.243 47.826 0.00 0.00 46.80 3.16
329 330 6.536582 CAGAACATGTAAAGATCAACTCCGAT 59.463 38.462 0.00 0.00 0.00 4.18
391 392 4.467438 TGCTGTTTGTAGAGATGAGGATGA 59.533 41.667 0.00 0.00 0.00 2.92
443 445 2.628178 AGCAATCATACGGATCCGAAGA 59.372 45.455 39.55 29.73 42.83 2.87
517 519 4.935352 ATGTGCACAAAATACAAGTGGT 57.065 36.364 25.72 0.00 33.98 4.16
656 658 9.745880 GTTCATAAGTTTAGGAGATCGAATACA 57.254 33.333 0.00 0.00 0.00 2.29
657 659 9.745880 TTCATAAGTTTAGGAGATCGAATACAC 57.254 33.333 0.00 0.00 0.00 2.90
658 660 8.074370 TCATAAGTTTAGGAGATCGAATACACG 58.926 37.037 0.00 0.00 0.00 4.49
660 662 4.643784 AGTTTAGGAGATCGAATACACGGT 59.356 41.667 0.00 0.00 0.00 4.83
661 663 5.824624 AGTTTAGGAGATCGAATACACGGTA 59.175 40.000 0.00 0.00 0.00 4.02
673 675 6.016527 TCGAATACACGGTAGCTCATAATCTT 60.017 38.462 0.00 0.00 0.00 2.40
716 718 1.071642 TTCGGCCGTCATGTTTGGA 59.928 52.632 27.15 0.00 0.00 3.53
719 721 1.024046 CGGCCGTCATGTTTGGATCA 61.024 55.000 19.50 0.00 0.00 2.92
721 723 0.099436 GCCGTCATGTTTGGATCAGC 59.901 55.000 0.00 0.00 0.00 4.26
747 749 9.117183 CCAATCTGATGATCTTCTTTTCATACA 57.883 33.333 9.75 0.00 32.84 2.29
787 789 7.771183 TGATTTAATAAAGCTTGGCGAGATTT 58.229 30.769 20.69 20.69 45.36 2.17
789 791 7.810766 TTTAATAAAGCTTGGCGAGATTTTG 57.189 32.000 21.90 0.00 40.93 2.44
792 794 1.168714 AGCTTGGCGAGATTTTGTCC 58.831 50.000 5.76 0.00 0.00 4.02
793 795 0.171231 GCTTGGCGAGATTTTGTCCC 59.829 55.000 5.76 0.00 0.00 4.46
871 873 6.074088 CGAATCCACAGCTCATAATAACTCAC 60.074 42.308 0.00 0.00 0.00 3.51
960 989 2.038975 TTCTCTCCCCTCCACCCG 59.961 66.667 0.00 0.00 0.00 5.28
961 990 4.779733 TCTCTCCCCTCCACCCGC 62.780 72.222 0.00 0.00 0.00 6.13
989 1018 2.107141 GCCGCTGCCGTATTCTCT 59.893 61.111 0.00 0.00 0.00 3.10
1062 1091 0.245539 CCGCTCCGTTTAGGTTCTGA 59.754 55.000 0.00 0.00 41.99 3.27
1200 1229 4.675671 CGGTGAGACAAACTCCTGATCTAC 60.676 50.000 0.00 0.00 44.34 2.59
1209 1238 0.894835 TCCTGATCTACGTTGCTGCA 59.105 50.000 0.00 0.00 0.00 4.41
1674 1746 4.266714 GAACGTTTGGGATTTATCAGGGA 58.733 43.478 0.46 0.00 0.00 4.20
1677 1749 3.371595 CGTTTGGGATTTATCAGGGACCT 60.372 47.826 0.00 0.00 0.00 3.85
1884 1959 3.843999 TGAATGCGAAAATTAGTTGGGC 58.156 40.909 0.00 0.00 0.00 5.36
1926 2001 6.650427 TTGTATACCGAGTCAAGAGCATAT 57.350 37.500 0.00 0.00 0.00 1.78
1938 2014 5.466058 GTCAAGAGCATATCAAGTCTGATGG 59.534 44.000 0.00 0.00 42.48 3.51
2110 2186 8.839343 CATTGCTCATCATATTAGTTTGTACCA 58.161 33.333 0.00 0.00 0.00 3.25
2124 2200 4.817318 TTGTACCACATCTACTGCATCA 57.183 40.909 0.00 0.00 0.00 3.07
2258 2353 7.015098 TCTCTGGAAGATTAGAAGCATCCTTAG 59.985 40.741 3.73 1.90 45.62 2.18
2337 2435 2.169352 CAGGCTTGCAGTCTGGTATACT 59.831 50.000 2.25 0.00 43.91 2.12
2338 2436 2.840651 AGGCTTGCAGTCTGGTATACTT 59.159 45.455 2.25 0.00 0.00 2.24
2339 2437 2.939103 GGCTTGCAGTCTGGTATACTTG 59.061 50.000 2.25 0.00 0.00 3.16
2340 2438 3.600388 GCTTGCAGTCTGGTATACTTGT 58.400 45.455 2.25 0.00 0.00 3.16
2341 2439 4.003648 GCTTGCAGTCTGGTATACTTGTT 58.996 43.478 2.25 0.00 0.00 2.83
2342 2440 5.175859 GCTTGCAGTCTGGTATACTTGTTA 58.824 41.667 2.25 0.00 0.00 2.41
2343 2441 5.642063 GCTTGCAGTCTGGTATACTTGTTAA 59.358 40.000 2.25 0.00 0.00 2.01
2415 2513 9.752961 GAACACTCCTAGAGTTAAATATCCTTC 57.247 37.037 0.00 0.00 41.37 3.46
2538 2636 5.067283 TGAGTCTTGTTGGTTAAAAGAAGGC 59.933 40.000 0.00 0.00 35.79 4.35
2820 2918 3.517500 TGGTCTTGCTCTTTTTGGGTTTT 59.482 39.130 0.00 0.00 0.00 2.43
2875 2974 7.113965 CAGAAGAAAAATTCCTTTGTCGATGTG 59.886 37.037 0.00 0.00 34.33 3.21
2937 3036 1.387756 CACCGTCGACCATTAACGAAC 59.612 52.381 10.58 0.00 40.12 3.95
3312 7233 7.492994 GGTCTGTATCTCTTTCCTGAATGTTAC 59.507 40.741 0.00 0.00 0.00 2.50
3352 7273 7.398332 AGGATTTAATTGGAATGGCCTATGATC 59.602 37.037 3.32 0.00 37.63 2.92
3829 7762 8.528044 TTGGTTTGTTTCTTATGGAAGTTACT 57.472 30.769 0.00 0.00 35.16 2.24
4048 7981 3.118075 TCCCACAAAATCCAGCGATATGA 60.118 43.478 0.00 0.00 0.00 2.15
4201 8134 8.484641 TGTCTTTTTCTCATCTCATGTACATC 57.515 34.615 5.07 0.00 0.00 3.06
4296 8229 1.374758 GACCTGTCCGGAGTGCAAG 60.375 63.158 3.06 0.00 36.31 4.01
4408 8341 4.082408 TCAACCGTGATGAGAACTATCGTT 60.082 41.667 0.00 0.00 35.68 3.85
4476 8409 4.702131 ACAGATGTGTTTTCTATTCCCTGC 59.298 41.667 0.00 0.00 30.30 4.85
4543 8481 4.324267 ACCTGCTAAATTCGTGCTTTACT 58.676 39.130 0.00 0.00 0.00 2.24
4560 8498 4.796038 TTACTGTTTCCTACTCCCTTCG 57.204 45.455 0.00 0.00 0.00 3.79
4596 8534 0.687427 AATTTGGGCCTGAATCCCCG 60.687 55.000 4.53 0.00 44.58 5.73
4670 8608 2.143122 AGTGTTGTACATGGCAGTTCG 58.857 47.619 0.00 0.00 0.00 3.95
4786 8724 3.634910 ACGGTTGCCAATTATCATTACCC 59.365 43.478 0.00 0.00 0.00 3.69
4864 8802 3.336138 GGCCCTACCTGAATAGCATAC 57.664 52.381 0.00 0.00 34.51 2.39
4865 8803 2.637872 GGCCCTACCTGAATAGCATACA 59.362 50.000 0.00 0.00 34.51 2.29
4866 8804 3.072476 GGCCCTACCTGAATAGCATACAA 59.928 47.826 0.00 0.00 34.51 2.41
4867 8805 4.445735 GGCCCTACCTGAATAGCATACAAA 60.446 45.833 0.00 0.00 34.51 2.83
4868 8806 4.515567 GCCCTACCTGAATAGCATACAAAC 59.484 45.833 0.00 0.00 0.00 2.93
4869 8807 5.687706 GCCCTACCTGAATAGCATACAAACT 60.688 44.000 0.00 0.00 0.00 2.66
4870 8808 5.760253 CCCTACCTGAATAGCATACAAACTG 59.240 44.000 0.00 0.00 0.00 3.16
4871 8809 6.349300 CCTACCTGAATAGCATACAAACTGT 58.651 40.000 0.00 0.00 0.00 3.55
4872 8810 6.823689 CCTACCTGAATAGCATACAAACTGTT 59.176 38.462 0.00 0.00 0.00 3.16
4873 8811 6.500684 ACCTGAATAGCATACAAACTGTTG 57.499 37.500 0.00 0.00 40.84 3.33
4874 8812 5.106157 ACCTGAATAGCATACAAACTGTTGC 60.106 40.000 0.00 0.00 38.39 4.17
4875 8813 5.106197 CCTGAATAGCATACAAACTGTTGCA 60.106 40.000 4.45 0.00 38.39 4.08
4876 8814 5.698832 TGAATAGCATACAAACTGTTGCAC 58.301 37.500 4.45 0.00 38.39 4.57
4877 8815 5.240403 TGAATAGCATACAAACTGTTGCACA 59.760 36.000 4.45 0.00 38.39 4.57
4878 8816 5.703978 ATAGCATACAAACTGTTGCACAA 57.296 34.783 4.45 0.00 38.39 3.33
4879 8817 4.589216 AGCATACAAACTGTTGCACAAT 57.411 36.364 4.45 0.00 38.39 2.71
4880 8818 5.703978 AGCATACAAACTGTTGCACAATA 57.296 34.783 4.45 0.00 38.39 1.90
4881 8819 5.460646 AGCATACAAACTGTTGCACAATAC 58.539 37.500 4.45 0.00 38.39 1.89
4882 8820 5.241506 AGCATACAAACTGTTGCACAATACT 59.758 36.000 4.45 0.00 38.39 2.12
4883 8821 5.569059 GCATACAAACTGTTGCACAATACTC 59.431 40.000 0.00 0.00 38.39 2.59
4884 8822 6.667370 CATACAAACTGTTGCACAATACTCA 58.333 36.000 0.00 0.00 38.39 3.41
4885 8823 5.574891 ACAAACTGTTGCACAATACTCAA 57.425 34.783 0.00 0.00 38.39 3.02
4886 8824 5.339990 ACAAACTGTTGCACAATACTCAAC 58.660 37.500 0.00 0.00 38.39 3.18
4887 8825 5.125417 ACAAACTGTTGCACAATACTCAACT 59.875 36.000 0.00 0.00 40.34 3.16
4888 8826 5.835113 AACTGTTGCACAATACTCAACTT 57.165 34.783 0.00 0.00 40.34 2.66
4889 8827 5.835113 ACTGTTGCACAATACTCAACTTT 57.165 34.783 6.01 0.00 40.34 2.66
4890 8828 5.581605 ACTGTTGCACAATACTCAACTTTG 58.418 37.500 6.01 0.00 40.34 2.77
4891 8829 5.125417 ACTGTTGCACAATACTCAACTTTGT 59.875 36.000 6.01 0.00 40.34 2.83
4892 8830 6.317642 ACTGTTGCACAATACTCAACTTTGTA 59.682 34.615 6.01 0.00 40.34 2.41
4893 8831 6.491394 TGTTGCACAATACTCAACTTTGTAC 58.509 36.000 6.01 0.00 40.34 2.90
4894 8832 6.094186 TGTTGCACAATACTCAACTTTGTACA 59.906 34.615 0.00 0.00 40.34 2.90
4895 8833 6.685527 TGCACAATACTCAACTTTGTACAA 57.314 33.333 3.59 3.59 32.57 2.41
4896 8834 7.089770 TGCACAATACTCAACTTTGTACAAA 57.910 32.000 19.53 19.53 32.57 2.83
4915 8853 9.554395 TGTACAAAGTTGAGTCATCTATTTTGA 57.446 29.630 15.99 3.46 38.91 2.69
4918 8856 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
4919 8857 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
4920 8858 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
4921 8859 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
4922 8860 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
4923 8861 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
4924 8862 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
4925 8863 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
4926 8864 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
4927 8865 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
4928 8866 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
4929 8867 5.974108 TCTATTTTGAAACGGAGGGAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
4930 8868 4.903045 ATTTTGAAACGGAGGGAGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
4931 8869 4.693042 TTTTGAAACGGAGGGAGTAGAA 57.307 40.909 0.00 0.00 0.00 2.10
4932 8870 4.903045 TTTGAAACGGAGGGAGTAGAAT 57.097 40.909 0.00 0.00 0.00 2.40
4933 8871 6.363167 TTTTGAAACGGAGGGAGTAGAATA 57.637 37.500 0.00 0.00 0.00 1.75
4934 8872 6.555463 TTTGAAACGGAGGGAGTAGAATAT 57.445 37.500 0.00 0.00 0.00 1.28
4935 8873 7.664552 TTTGAAACGGAGGGAGTAGAATATA 57.335 36.000 0.00 0.00 0.00 0.86
4936 8874 6.896021 TGAAACGGAGGGAGTAGAATATAG 57.104 41.667 0.00 0.00 0.00 1.31
4937 8875 6.607970 TGAAACGGAGGGAGTAGAATATAGA 58.392 40.000 0.00 0.00 0.00 1.98
5237 9204 1.234615 TAGCTGCAGAACAAACCCGC 61.235 55.000 20.43 0.00 0.00 6.13
5262 9229 0.981183 AGGTCGGCTCATGGTTAACA 59.019 50.000 8.10 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.303561 ATTTGCTCAGGCGCCAGAA 60.304 52.632 31.54 10.36 42.25 3.02
55 56 4.217334 TCATAAACAGCCATTCTTTCGCAA 59.783 37.500 0.00 0.00 0.00 4.85
177 178 5.690865 ACAGTGGATTGACAAAGGACTTTA 58.309 37.500 0.00 0.00 0.00 1.85
221 222 3.270027 CCTTGTTAATGCCGAGATGTCA 58.730 45.455 0.00 0.00 0.00 3.58
241 242 2.087646 GATTCTGACTCTGGTTTGGCC 58.912 52.381 0.00 0.00 37.90 5.36
329 330 0.662619 CGTTCCTGAAAACAGCTGCA 59.337 50.000 15.27 2.21 0.00 4.41
350 351 3.467226 GCTACAGCCCCACCGCTA 61.467 66.667 0.00 0.00 36.82 4.26
391 392 3.066342 CGCATGATGCTCCAGAAAAATCT 59.934 43.478 16.17 0.00 42.25 2.40
414 416 3.130633 TCCGTATGATTGCTACATGTGC 58.869 45.455 9.11 10.76 0.00 4.57
420 422 3.570926 TCGGATCCGTATGATTGCTAC 57.429 47.619 32.15 0.00 40.74 3.58
443 445 5.717178 TCTCACTACCATTGCTTCTAGAGTT 59.283 40.000 0.00 0.00 0.00 3.01
534 536 3.187700 CCTGCTGTATTCCGTAGACAAC 58.812 50.000 0.00 0.00 0.00 3.32
596 598 9.482627 CAAGAAGTAAAAGTATGAGAACAGTCT 57.517 33.333 0.00 0.00 36.55 3.24
636 638 5.126707 ACCGTGTATTCGATCTCCTAAACTT 59.873 40.000 0.00 0.00 0.00 2.66
656 658 5.531122 TTAGCAAGATTATGAGCTACCGT 57.469 39.130 0.00 0.00 39.11 4.83
657 659 4.387256 GCTTAGCAAGATTATGAGCTACCG 59.613 45.833 0.00 0.00 39.11 4.02
658 660 5.300752 TGCTTAGCAAGATTATGAGCTACC 58.699 41.667 3.67 0.00 39.11 3.18
660 662 5.410746 GCATGCTTAGCAAGATTATGAGCTA 59.589 40.000 12.08 0.00 43.62 3.32
661 663 4.215827 GCATGCTTAGCAAGATTATGAGCT 59.784 41.667 12.08 0.00 43.62 4.09
673 675 4.381825 CCCAATGTTAAAGCATGCTTAGCA 60.382 41.667 32.12 27.26 44.86 3.49
719 721 6.185511 TGAAAAGAAGATCATCAGATTGGCT 58.814 36.000 0.10 0.00 33.72 4.75
721 723 9.117183 TGTATGAAAAGAAGATCATCAGATTGG 57.883 33.333 0.10 0.00 37.46 3.16
1062 1091 2.385803 ACCCTAGAATCGAACCGACAT 58.614 47.619 0.00 0.00 39.18 3.06
1200 1229 5.909054 CAGGTAATAATAACATGCAGCAACG 59.091 40.000 0.00 0.00 0.00 4.10
1209 1238 8.732746 AGCGAAAAGACAGGTAATAATAACAT 57.267 30.769 0.00 0.00 0.00 2.71
1316 1345 7.916914 AGCAAAACCGTTATTAATACACTCT 57.083 32.000 0.00 0.00 0.00 3.24
1401 1470 9.677567 CGATCCCATTTATACGAAATGAAAAAT 57.322 29.630 10.79 0.85 39.36 1.82
1482 1554 4.241681 GTTGCCATGCTTAAAATCCGAAA 58.758 39.130 0.00 0.00 0.00 3.46
1528 1600 0.813610 TGCCAACCTCACGTGAACTG 60.814 55.000 20.49 15.53 0.00 3.16
1530 1602 0.736053 TTTGCCAACCTCACGTGAAC 59.264 50.000 20.49 5.66 0.00 3.18
1574 1646 1.281656 GCAACTTTGTCCCGGTTCG 59.718 57.895 0.00 0.00 0.00 3.95
1579 1651 0.240945 GACATGGCAACTTTGTCCCG 59.759 55.000 7.56 0.00 41.58 5.14
1772 1844 4.459337 CCTCAAAATTTCTACAGGTGGACC 59.541 45.833 0.00 0.00 0.00 4.46
1938 2014 2.224670 TGTGTGGGTCAAGGGTATCAAC 60.225 50.000 0.00 0.00 0.00 3.18
1985 2061 4.624015 TCCAGTACCGTTACAGAAAACTG 58.376 43.478 0.00 0.00 34.15 3.16
2110 2186 4.428209 CGAGAACTTGATGCAGTAGATGT 58.572 43.478 0.00 0.00 0.00 3.06
2124 2200 1.645710 ACTGATCCACCCGAGAACTT 58.354 50.000 0.00 0.00 0.00 2.66
2266 2363 4.142902 CGTGATGACGCTTTACATTCCTTT 60.143 41.667 0.00 0.00 39.10 3.11
2267 2364 3.370978 CGTGATGACGCTTTACATTCCTT 59.629 43.478 0.00 0.00 39.10 3.36
2282 2379 7.876068 AGGAAAGTCTATTTTTGTACGTGATGA 59.124 33.333 0.00 0.00 0.00 2.92
2289 2386 6.015772 TGGCCAAGGAAAGTCTATTTTTGTAC 60.016 38.462 0.61 0.00 0.00 2.90
2337 2435 6.030849 CCGGCGATGAAATAACAATTAACAA 58.969 36.000 9.30 0.00 0.00 2.83
2338 2436 5.124138 ACCGGCGATGAAATAACAATTAACA 59.876 36.000 9.30 0.00 0.00 2.41
2339 2437 5.575019 ACCGGCGATGAAATAACAATTAAC 58.425 37.500 9.30 0.00 0.00 2.01
2340 2438 5.821516 ACCGGCGATGAAATAACAATTAA 57.178 34.783 9.30 0.00 0.00 1.40
2341 2439 5.236911 GGTACCGGCGATGAAATAACAATTA 59.763 40.000 9.30 0.00 0.00 1.40
2342 2440 4.035909 GGTACCGGCGATGAAATAACAATT 59.964 41.667 9.30 0.00 0.00 2.32
2343 2441 3.562557 GGTACCGGCGATGAAATAACAAT 59.437 43.478 9.30 0.00 0.00 2.71
2538 2636 7.976734 CCCTTACAGACACTGAAAATAGTAGAG 59.023 40.741 5.76 0.00 35.18 2.43
2961 3060 9.851686 TTATATCAAAGACTAAGCAACCATCAT 57.148 29.630 0.00 0.00 0.00 2.45
3069 3168 1.647629 CGCTGGCATCATTCTCTGC 59.352 57.895 0.00 0.00 37.66 4.26
3312 7233 7.277098 CCAATTAAATCCTGAAATGACTGCAAG 59.723 37.037 0.00 0.00 42.29 4.01
3352 7273 5.566469 TCCCTACAACAATTAACAAGAGGG 58.434 41.667 0.00 0.00 42.19 4.30
3829 7762 3.136443 CAGTCCATCTGGGCCTATAAACA 59.864 47.826 4.53 0.00 41.83 2.83
4048 7981 6.293081 GCACAATATCTACGAGTGATGCAAAT 60.293 38.462 0.00 0.00 32.14 2.32
4201 8134 0.907486 TGCAGGAGGAGGATGAGTTG 59.093 55.000 0.00 0.00 0.00 3.16
4243 8176 1.537202 GGCATCTTTGTCTTTGCGAGT 59.463 47.619 0.00 0.00 35.95 4.18
4296 8229 1.066358 CGGAAGGGGTAGTTCAGGTTC 60.066 57.143 0.00 0.00 0.00 3.62
4408 8341 3.009033 AGCTAGGGTACAACAATGCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
4468 8401 1.474077 GAATGCTTGTTCGCAGGGAAT 59.526 47.619 2.78 0.00 44.10 3.01
4476 8409 6.520175 CATAGTCGATATGAATGCTTGTTCG 58.480 40.000 8.36 0.00 43.54 3.95
4543 8481 2.764572 GGATCGAAGGGAGTAGGAAACA 59.235 50.000 0.00 0.00 0.00 2.83
4560 8498 9.489084 GGCCCAAATTTAAATTAGTTATGGATC 57.511 33.333 22.09 15.39 0.00 3.36
4596 8534 1.929836 CTATGACAGCAAGCGTTCCTC 59.070 52.381 0.00 0.00 0.00 3.71
4670 8608 8.878769 TCTAAAGAAATTTGCCTCAAAACAAAC 58.121 29.630 0.00 0.00 38.50 2.93
4786 8724 6.749118 GGAGCTCACTGCATGTAAATTTAAAG 59.251 38.462 17.19 0.00 45.94 1.85
4870 8808 6.491394 TGTACAAAGTTGAGTATTGTGCAAC 58.509 36.000 6.25 0.00 43.42 4.17
4871 8809 6.685527 TGTACAAAGTTGAGTATTGTGCAA 57.314 33.333 6.25 0.00 43.42 4.08
4872 8810 6.685527 TTGTACAAAGTTGAGTATTGTGCA 57.314 33.333 5.64 4.86 44.24 4.57
4873 8811 7.608974 CTTTGTACAAAGTTGAGTATTGTGC 57.391 36.000 31.55 0.00 42.02 4.57
4889 8827 9.554395 TCAAAATAGATGACTCAACTTTGTACA 57.446 29.630 0.00 0.00 0.00 2.90
4892 8830 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
4893 8831 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
4894 8832 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
4895 8833 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
4896 8834 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
4897 8835 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
4898 8836 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
4899 8837 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
4900 8838 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
4901 8839 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
4902 8840 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
4903 8841 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
4904 8842 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
4905 8843 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
4906 8844 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
4907 8845 5.974108 TCTACTCCCTCCGTTTCAAAATAG 58.026 41.667 0.00 0.00 0.00 1.73
4908 8846 6.363167 TTCTACTCCCTCCGTTTCAAAATA 57.637 37.500 0.00 0.00 0.00 1.40
4909 8847 4.903045 TCTACTCCCTCCGTTTCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
4910 8848 4.693042 TTCTACTCCCTCCGTTTCAAAA 57.307 40.909 0.00 0.00 0.00 2.44
4911 8849 4.903045 ATTCTACTCCCTCCGTTTCAAA 57.097 40.909 0.00 0.00 0.00 2.69
4912 8850 7.064866 TCTATATTCTACTCCCTCCGTTTCAA 58.935 38.462 0.00 0.00 0.00 2.69
4913 8851 6.607970 TCTATATTCTACTCCCTCCGTTTCA 58.392 40.000 0.00 0.00 0.00 2.69
4914 8852 7.521871 TTCTATATTCTACTCCCTCCGTTTC 57.478 40.000 0.00 0.00 0.00 2.78
4915 8853 7.951245 AGATTCTATATTCTACTCCCTCCGTTT 59.049 37.037 0.00 0.00 0.00 3.60
4916 8854 7.471890 AGATTCTATATTCTACTCCCTCCGTT 58.528 38.462 0.00 0.00 0.00 4.44
4917 8855 7.034967 AGATTCTATATTCTACTCCCTCCGT 57.965 40.000 0.00 0.00 0.00 4.69
4918 8856 7.948034 AAGATTCTATATTCTACTCCCTCCG 57.052 40.000 0.00 0.00 0.00 4.63
4919 8857 8.038351 GCAAAGATTCTATATTCTACTCCCTCC 58.962 40.741 0.00 0.00 0.00 4.30
4920 8858 8.589338 TGCAAAGATTCTATATTCTACTCCCTC 58.411 37.037 0.00 0.00 0.00 4.30
4921 8859 8.497910 TGCAAAGATTCTATATTCTACTCCCT 57.502 34.615 0.00 0.00 0.00 4.20
4922 8860 9.377312 GATGCAAAGATTCTATATTCTACTCCC 57.623 37.037 0.00 0.00 0.00 4.30
4923 8861 9.377312 GGATGCAAAGATTCTATATTCTACTCC 57.623 37.037 0.00 0.00 0.00 3.85
4924 8862 9.377312 GGGATGCAAAGATTCTATATTCTACTC 57.623 37.037 0.00 0.00 0.00 2.59
4925 8863 9.110382 AGGGATGCAAAGATTCTATATTCTACT 57.890 33.333 0.00 0.00 0.00 2.57
4928 8866 8.325046 GGTAGGGATGCAAAGATTCTATATTCT 58.675 37.037 0.00 0.00 0.00 2.40
4929 8867 8.325046 AGGTAGGGATGCAAAGATTCTATATTC 58.675 37.037 0.00 0.00 0.00 1.75
4930 8868 8.224620 AGGTAGGGATGCAAAGATTCTATATT 57.775 34.615 0.00 0.00 0.00 1.28
4931 8869 7.092668 GGAGGTAGGGATGCAAAGATTCTATAT 60.093 40.741 0.00 0.00 0.00 0.86
4932 8870 6.213600 GGAGGTAGGGATGCAAAGATTCTATA 59.786 42.308 0.00 0.00 0.00 1.31
4933 8871 5.013599 GGAGGTAGGGATGCAAAGATTCTAT 59.986 44.000 0.00 0.00 0.00 1.98
4934 8872 4.348168 GGAGGTAGGGATGCAAAGATTCTA 59.652 45.833 0.00 0.00 0.00 2.10
4935 8873 3.137360 GGAGGTAGGGATGCAAAGATTCT 59.863 47.826 0.00 0.00 0.00 2.40
4936 8874 3.481453 GGAGGTAGGGATGCAAAGATTC 58.519 50.000 0.00 0.00 0.00 2.52
4937 8875 2.175715 GGGAGGTAGGGATGCAAAGATT 59.824 50.000 0.00 0.00 0.00 2.40
5237 9204 1.202533 ACCATGAGCCGACCTAATTCG 60.203 52.381 0.00 0.00 38.80 3.34
5262 9229 2.224426 TGGTTACACCATCTTCGCTGTT 60.224 45.455 0.00 0.00 44.79 3.16
5277 9244 4.575885 TGAACAAGCTGGATAGTGGTTAC 58.424 43.478 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.