Multiple sequence alignment - TraesCS2D01G176200

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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 TraesCS2D01G176200 chr2D 100.000 9456 0 0 1 9456 119668936 119659481 0.000000e+00 17463
1 TraesCS2D01G176200 chr2A 95.577 9428 256 54 4 9363 122015528 122006194 0.000000e+00 14951
2 TraesCS2D01G176200 chr2B 97.126 4140 80 10 3531 7637 172000955 171996822 0.000000e+00 6950
3 TraesCS2D01G176200 chr2B 89.175 3575 218 63 7 3530 172004463 172001007 0.000000e+00 4301
4 TraesCS2D01G176200 chr2B 93.828 1280 41 24 7718 8972 171996791 171995525 0.000000e+00 1892
5 TraesCS2D01G176200 chr2B 98.305 59 1 0 9398 9456 171995170 171995112 4.670000e-18 104
6 TraesCS2D01G176200 chr1D 82.105 380 56 7 2563 2934 411173207 411172832 1.980000e-81 315
7 TraesCS2D01G176200 chr4D 82.547 212 24 9 1173 1378 3860429 3860633 3.510000e-39 174
8 TraesCS2D01G176200 chr7D 90.816 98 9 0 1281 1378 28527908 28528005 2.140000e-26 132


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 TraesCS2D01G176200 chr2D 119659481 119668936 9455 True 17463.00 17463 100.0000 1 9456 1 chr2D.!!$R1 9455
1 TraesCS2D01G176200 chr2A 122006194 122015528 9334 True 14951.00 14951 95.5770 4 9363 1 chr2A.!!$R1 9359
2 TraesCS2D01G176200 chr2B 171995112 172004463 9351 True 3311.75 6950 94.6085 7 9456 4 chr2B.!!$R1 9449


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
694 714 0.106217 GGAGGAGAGACAGAGAGGGG 60.106 65.000 0.00 0.0 0.00 4.79 F
1145 1181 1.079266 GGCTGGCTGACTGACTCTG 60.079 63.158 0.00 0.0 0.00 3.35 F
1147 1183 1.595882 CTGGCTGACTGACTCTGGG 59.404 63.158 0.00 0.0 0.00 4.45 F
2107 2144 2.595386 GCTCATTTACCTTGTTTGCCG 58.405 47.619 0.00 0.0 0.00 5.69 F
2122 2159 5.098893 TGTTTGCCGGATAAAATTGATTCG 58.901 37.500 5.05 0.0 0.00 3.34 F
3459 3521 5.235186 CACCCATCGTGAAGTTATCAATCTC 59.765 44.000 0.00 0.0 46.20 2.75 F
4568 4684 2.160205 GGAGTTAACCAAGGACAAGGC 58.840 52.381 0.88 0.0 0.00 4.35 F
4902 5021 1.130373 TCAAATCGAAAGCCACATCGC 59.870 47.619 0.00 0.0 38.87 4.58 F
6279 6398 1.298014 AGCTACTGCAAGGGCTCAC 59.702 57.895 1.80 0.0 41.84 3.51 F
7041 7160 1.651240 ATGCATCTCAACAGCCACGC 61.651 55.000 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2009 1.562942 TCCAGAAGGCAGAAGCATCAT 59.437 47.619 0.00 0.0 44.61 2.45 R
2684 2740 1.699634 ACCACAACACAGCCTACAGAT 59.300 47.619 0.00 0.0 0.00 2.90 R
2736 2792 6.012858 TGGATGGTTAAGATAGTTCAGGTTGT 60.013 38.462 0.00 0.0 0.00 3.32 R
3376 3434 1.684248 GCTTCCACCATCCAGCATCTT 60.684 52.381 0.00 0.0 32.17 2.40 R
3492 3554 2.595380 ACCCACCCTCCTAATTCCTAGA 59.405 50.000 0.00 0.0 0.00 2.43 R
4575 4691 0.110056 GCAACATGCTCTGACAACCG 60.110 55.000 0.00 0.0 40.96 4.44 R
5782 5901 1.826385 ACAGAGTACAGCATTTGGGC 58.174 50.000 0.00 0.0 0.00 5.36 R
6747 6866 1.334689 GCTTCCCGTGGAAAAGAAACG 60.335 52.381 6.79 0.0 41.54 3.60 R
7841 7986 0.704664 AGGGAGTTGGAATTGGGGAC 59.295 55.000 0.00 0.0 0.00 4.46 R
8906 9084 0.252375 GGGGCCCCATTATGCATCAT 60.252 55.000 37.61 0.0 35.81 2.45 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
101 102 0.761187 ATCATGGCTGGCTACATCGT 59.239 50.000 2.00 0.00 0.00 3.73
124 125 8.995220 TCGTAGTACTAGTTTTCATGCAAAAAT 58.005 29.630 1.87 1.12 35.68 1.82
181 189 2.285834 GCTGACGCCGAAAGATATGTTG 60.286 50.000 0.00 0.00 0.00 3.33
182 190 2.276201 TGACGCCGAAAGATATGTTGG 58.724 47.619 0.00 0.00 0.00 3.77
183 191 2.277084 GACGCCGAAAGATATGTTGGT 58.723 47.619 0.00 0.00 0.00 3.67
184 192 3.119065 TGACGCCGAAAGATATGTTGGTA 60.119 43.478 0.00 0.00 0.00 3.25
185 193 3.192466 ACGCCGAAAGATATGTTGGTAC 58.808 45.455 0.00 0.00 0.00 3.34
189 197 5.598769 GCCGAAAGATATGTTGGTACTAGT 58.401 41.667 0.00 0.00 0.00 2.57
309 320 9.295825 TCAATAATTAAGACAGAACCAACACAT 57.704 29.630 0.00 0.00 0.00 3.21
329 340 0.321671 CCACCATCCTCGTGTCAGTT 59.678 55.000 0.00 0.00 0.00 3.16
340 351 0.316196 GTGTCAGTTGCAACGACAGC 60.316 55.000 35.48 28.74 40.37 4.40
348 359 1.014044 TGCAACGACAGCGATCCTTC 61.014 55.000 0.00 0.00 41.64 3.46
352 363 0.888619 ACGACAGCGATCCTTCTTCA 59.111 50.000 0.00 0.00 41.64 3.02
381 392 4.346709 TCCCTCCTCCAAAATTCAAAAACC 59.653 41.667 0.00 0.00 0.00 3.27
397 408 1.566298 AACCAGAGCCCCTCATCCAC 61.566 60.000 0.00 0.00 32.06 4.02
403 414 1.201429 AGCCCCTCATCCACTTTCGT 61.201 55.000 0.00 0.00 0.00 3.85
561 578 7.166804 GCAACAATCTCTCGTAATCTCTCTTAC 59.833 40.741 0.00 0.00 0.00 2.34
562 579 8.402472 CAACAATCTCTCGTAATCTCTCTTACT 58.598 37.037 0.00 0.00 30.88 2.24
563 580 8.514330 ACAATCTCTCGTAATCTCTCTTACTT 57.486 34.615 0.00 0.00 30.88 2.24
564 581 9.616156 ACAATCTCTCGTAATCTCTCTTACTTA 57.384 33.333 0.00 0.00 30.88 2.24
591 608 1.679032 CCTAAGCTCCCCCAAAACTCG 60.679 57.143 0.00 0.00 0.00 4.18
625 642 0.845102 AATCTCCCCGAAACACCCCT 60.845 55.000 0.00 0.00 0.00 4.79
685 702 2.737039 GCATTTCTCACGGAGGAGAGAC 60.737 54.545 4.32 0.00 44.23 3.36
694 714 0.106217 GGAGGAGAGACAGAGAGGGG 60.106 65.000 0.00 0.00 0.00 4.79
735 755 1.675415 CCAAACCAGCAGAGCTCTCTC 60.675 57.143 14.96 8.89 36.40 3.20
1099 1135 4.129148 GGGGATGCCTCGCCCTTT 62.129 66.667 13.29 0.00 46.28 3.11
1144 1180 1.534959 TGGCTGGCTGACTGACTCT 60.535 57.895 2.00 0.00 0.00 3.24
1145 1181 1.079266 GGCTGGCTGACTGACTCTG 60.079 63.158 0.00 0.00 0.00 3.35
1147 1183 1.595882 CTGGCTGACTGACTCTGGG 59.404 63.158 0.00 0.00 0.00 4.45
1178 1214 4.057428 GCGAGCTCGTGGTGTCCT 62.057 66.667 34.46 0.00 42.22 3.85
1729 1766 3.244561 ACACTCGTTCATCATGGGAAACT 60.245 43.478 0.00 0.00 0.00 2.66
1730 1767 4.020573 ACACTCGTTCATCATGGGAAACTA 60.021 41.667 0.00 0.00 0.00 2.24
2107 2144 2.595386 GCTCATTTACCTTGTTTGCCG 58.405 47.619 0.00 0.00 0.00 5.69
2122 2159 5.098893 TGTTTGCCGGATAAAATTGATTCG 58.901 37.500 5.05 0.00 0.00 3.34
2132 2176 8.895845 CGGATAAAATTGATTCGATTCACAATC 58.104 33.333 9.43 8.14 32.84 2.67
2154 2198 9.878599 CAATCAGTTTGTACTTTGTTAAGTAGG 57.121 33.333 0.00 0.00 45.12 3.18
2281 2325 7.495934 TCATGTTAGCTGCTTTCTATAACCTTC 59.504 37.037 7.79 0.00 0.00 3.46
2401 2446 6.035975 TCTGTGATTACATATCGTGCACTTTG 59.964 38.462 16.19 9.19 35.97 2.77
2746 2802 6.887626 TCACCCTTTTAATACAACCTGAAC 57.112 37.500 0.00 0.00 0.00 3.18
3211 3268 7.147976 GTGCTCAAGTTATCCTTTTTGACATT 58.852 34.615 0.00 0.00 0.00 2.71
3437 3499 9.274206 AGAACTCAAGTTTAGGAAATAACTCAC 57.726 33.333 0.00 0.00 38.56 3.51
3438 3500 7.981102 ACTCAAGTTTAGGAAATAACTCACC 57.019 36.000 0.00 0.00 33.66 4.02
3441 3503 7.466804 TCAAGTTTAGGAAATAACTCACCCAT 58.533 34.615 0.00 0.00 33.66 4.00
3443 3505 6.113411 AGTTTAGGAAATAACTCACCCATCG 58.887 40.000 0.00 0.00 28.79 3.84
3459 3521 5.235186 CACCCATCGTGAAGTTATCAATCTC 59.765 44.000 0.00 0.00 46.20 2.75
3492 3554 3.584733 AGTTTGCAGGAGAAGGTTCTT 57.415 42.857 0.00 0.00 37.73 2.52
3493 3555 3.481453 AGTTTGCAGGAGAAGGTTCTTC 58.519 45.455 0.00 0.00 37.73 2.87
3520 3582 2.953093 TAGGAGGGTGGGTCATGTTA 57.047 50.000 0.00 0.00 0.00 2.41
3563 3676 5.236655 TGATATCTTCTGTCACAGTCGTC 57.763 43.478 4.28 0.00 32.61 4.20
3793 3909 4.526262 AGACATGTCTATAGATGAGCCACC 59.474 45.833 26.87 0.00 38.35 4.61
3865 3981 3.859961 CCGCATACCGATAGATTAAGCAG 59.140 47.826 0.00 0.00 40.02 4.24
3971 4087 3.476552 AGAAAACGAAACTGATGCTCCA 58.523 40.909 0.00 0.00 0.00 3.86
3972 4088 3.882888 AGAAAACGAAACTGATGCTCCAA 59.117 39.130 0.00 0.00 0.00 3.53
4160 4276 3.556213 CGTCCATGGACAAGTTGGTAAGA 60.556 47.826 37.42 0.57 44.77 2.10
4313 4429 3.959535 AGAGCTGATAAGGATGCTAGC 57.040 47.619 8.10 8.10 35.76 3.42
4361 4477 2.557317 TCTTGGTCACGTCAAAAGGAC 58.443 47.619 0.00 0.00 43.36 3.85
4419 4535 5.390991 GCTTCTTCGTCCTCAACCTTTAATG 60.391 44.000 0.00 0.00 0.00 1.90
4455 4571 5.132502 CCTCATTATCAGCCATTGTTACCA 58.867 41.667 0.00 0.00 0.00 3.25
4568 4684 2.160205 GGAGTTAACCAAGGACAAGGC 58.840 52.381 0.88 0.00 0.00 4.35
4575 4691 1.507141 CCAAGGACAAGGCGACACAC 61.507 60.000 0.00 0.00 0.00 3.82
4666 4782 3.660501 GGAAGCTTTCCCGAAACATTT 57.339 42.857 0.00 0.00 44.30 2.32
4877 4996 1.746787 GGGAAAACGTCAAGTGGTGTT 59.253 47.619 0.00 0.00 0.00 3.32
4889 5008 4.452114 TCAAGTGGTGTTGATCTCAAATCG 59.548 41.667 0.00 0.00 37.63 3.34
4901 5020 2.672874 TCTCAAATCGAAAGCCACATCG 59.327 45.455 0.00 0.00 40.31 3.84
4902 5021 1.130373 TCAAATCGAAAGCCACATCGC 59.870 47.619 0.00 0.00 38.87 4.58
5059 5178 4.263905 TGGGTCTGAAATACTGCCTCAATT 60.264 41.667 0.00 0.00 0.00 2.32
5327 5446 3.361281 ACAGATGCACAGGTTGATGAT 57.639 42.857 0.00 0.00 0.00 2.45
5724 5843 7.437748 AGATTCTACATGGATTAGTGCTGTAC 58.562 38.462 0.00 0.00 0.00 2.90
5725 5844 6.791867 TTCTACATGGATTAGTGCTGTACT 57.208 37.500 3.41 3.41 43.56 2.73
5726 5845 6.791867 TCTACATGGATTAGTGCTGTACTT 57.208 37.500 3.17 0.00 40.89 2.24
6153 6272 1.544691 TCGTCAAGAGCTGTAAGACCC 59.455 52.381 9.78 0.00 34.07 4.46
6279 6398 1.298014 AGCTACTGCAAGGGCTCAC 59.702 57.895 1.80 0.00 41.84 3.51
6747 6866 1.672881 CCAGGATCAGAAAATGGCGAC 59.327 52.381 0.00 0.00 0.00 5.19
7041 7160 1.651240 ATGCATCTCAACAGCCACGC 61.651 55.000 0.00 0.00 0.00 5.34
7322 7441 9.985318 GCATGCTATTTCAAGTATCATATCTTC 57.015 33.333 11.37 0.00 0.00 2.87
7408 7527 2.187958 TGTCCCCCATGACAACTAGAG 58.812 52.381 0.00 0.00 42.06 2.43
7461 7580 4.933400 TCCAACGCTTCTTTCCATACTTAC 59.067 41.667 0.00 0.00 0.00 2.34
7520 7665 7.098477 TCATGTTTCCAGATAAAAGCAAATGG 58.902 34.615 0.00 0.00 0.00 3.16
7639 7784 7.094933 ACCAGATAAATTAAAGTGACGGTGAAC 60.095 37.037 0.00 0.00 0.00 3.18
7640 7785 7.119262 CCAGATAAATTAAAGTGACGGTGAACT 59.881 37.037 0.00 0.00 0.00 3.01
7661 7806 8.372459 TGAACTAGTTACTTTATCCTTGCTGAA 58.628 33.333 8.42 0.00 0.00 3.02
7721 7866 7.105241 AGCCTTGGAATCAATTGTTTCTATC 57.895 36.000 22.37 11.17 31.75 2.08
7722 7867 6.097412 AGCCTTGGAATCAATTGTTTCTATCC 59.903 38.462 22.37 11.75 31.75 2.59
7723 7868 6.097412 GCCTTGGAATCAATTGTTTCTATCCT 59.903 38.462 22.37 0.00 31.75 3.24
7724 7869 7.364144 GCCTTGGAATCAATTGTTTCTATCCTT 60.364 37.037 22.37 0.00 31.75 3.36
7725 7870 7.977853 CCTTGGAATCAATTGTTTCTATCCTTG 59.022 37.037 22.37 8.80 31.75 3.61
7726 7871 7.408756 TGGAATCAATTGTTTCTATCCTTGG 57.591 36.000 22.37 0.00 0.00 3.61
7727 7872 7.181361 TGGAATCAATTGTTTCTATCCTTGGA 58.819 34.615 22.37 0.00 0.00 3.53
7728 7873 7.673504 TGGAATCAATTGTTTCTATCCTTGGAA 59.326 33.333 22.37 0.00 0.00 3.53
7729 7874 8.699130 GGAATCAATTGTTTCTATCCTTGGAAT 58.301 33.333 22.37 0.00 0.00 3.01
7730 7875 9.741647 GAATCAATTGTTTCTATCCTTGGAATC 57.258 33.333 18.08 0.00 0.00 2.52
7731 7876 8.827832 ATCAATTGTTTCTATCCTTGGAATCA 57.172 30.769 5.13 0.00 0.00 2.57
7732 7877 8.648698 TCAATTGTTTCTATCCTTGGAATCAA 57.351 30.769 5.13 0.00 36.83 2.57
7733 7878 9.258629 TCAATTGTTTCTATCCTTGGAATCAAT 57.741 29.630 5.13 0.00 41.06 2.57
7734 7879 9.880157 CAATTGTTTCTATCCTTGGAATCAATT 57.120 29.630 13.94 13.94 44.70 2.32
7735 7880 9.880157 AATTGTTTCTATCCTTGGAATCAATTG 57.120 29.630 16.75 0.00 43.56 2.32
7736 7881 6.866480 TGTTTCTATCCTTGGAATCAATTGC 58.134 36.000 0.00 0.00 31.75 3.56
7737 7882 6.664816 TGTTTCTATCCTTGGAATCAATTGCT 59.335 34.615 0.00 0.00 31.75 3.91
7738 7883 7.178983 TGTTTCTATCCTTGGAATCAATTGCTT 59.821 33.333 0.00 0.00 31.75 3.91
7739 7884 6.949352 TCTATCCTTGGAATCAATTGCTTC 57.051 37.500 12.58 12.58 31.75 3.86
7740 7885 6.666678 TCTATCCTTGGAATCAATTGCTTCT 58.333 36.000 18.64 3.88 31.75 2.85
7741 7886 7.805163 TCTATCCTTGGAATCAATTGCTTCTA 58.195 34.615 18.64 12.00 31.75 2.10
7742 7887 8.443176 TCTATCCTTGGAATCAATTGCTTCTAT 58.557 33.333 18.64 9.40 31.75 1.98
7841 7986 9.447040 CTCTTTGCACTGATCATATTTATGTTG 57.553 33.333 0.00 0.00 35.26 3.33
8006 8151 9.301153 GTTTTGTGTATGGGAATGATACATTTC 57.699 33.333 0.00 0.00 38.30 2.17
8059 8204 5.690857 ACTTTTGAGTCTTAAGCTGTACGTC 59.309 40.000 0.00 0.00 0.00 4.34
8290 8466 4.640201 GCTGCTCAATTAGAACATAACCCA 59.360 41.667 0.00 0.00 0.00 4.51
8296 8472 7.283127 GCTCAATTAGAACATAACCCATGAAGA 59.717 37.037 0.00 0.00 38.10 2.87
8301 8477 5.440610 AGAACATAACCCATGAAGATGACC 58.559 41.667 0.00 0.00 38.10 4.02
8525 8702 8.575649 AGGTAAAGATATCAAATTTTCACGGT 57.424 30.769 5.32 0.00 0.00 4.83
8682 8860 4.994282 TGTGTAGAGTTGGACTCCTAGAA 58.006 43.478 4.56 0.00 46.18 2.10
8683 8861 4.765856 TGTGTAGAGTTGGACTCCTAGAAC 59.234 45.833 4.56 0.00 46.18 3.01
8797 8975 7.028361 TGTTTCGTCGTTCACACACATATATA 58.972 34.615 0.00 0.00 0.00 0.86
8798 8976 7.703197 TGTTTCGTCGTTCACACACATATATAT 59.297 33.333 0.00 0.00 0.00 0.86
8906 9084 3.621268 GCATTTCTTGTACAGGCGACATA 59.379 43.478 0.00 0.00 0.00 2.29
8995 9298 0.991146 ATTTGGAATGTTTGGGGCCC 59.009 50.000 18.17 18.17 0.00 5.80
9050 9353 2.674796 AACGAGTTGTATCCTCTGCC 57.325 50.000 0.00 0.00 0.00 4.85
9107 9438 1.210478 GGGGTGAATTGCTCTGCTCTA 59.790 52.381 0.00 0.00 0.00 2.43
9171 9519 2.154462 CCAGTCCGTGCTCTTTCAAAT 58.846 47.619 0.00 0.00 0.00 2.32
9178 9526 2.662791 CGTGCTCTTTCAAATGACCACG 60.663 50.000 10.25 10.25 36.51 4.94
9207 9555 3.756434 TCAAAATTGTGACGGGATTCTCC 59.244 43.478 0.00 0.00 35.23 3.71
9220 9568 4.217767 CGGGATTCTCCGTTCAGATATACA 59.782 45.833 5.67 0.00 44.60 2.29
9221 9569 5.278808 CGGGATTCTCCGTTCAGATATACAA 60.279 44.000 5.67 0.00 44.60 2.41
9222 9570 6.159988 GGGATTCTCCGTTCAGATATACAAG 58.840 44.000 0.00 0.00 37.43 3.16
9223 9571 6.239345 GGGATTCTCCGTTCAGATATACAAGT 60.239 42.308 0.00 0.00 37.43 3.16
9224 9572 6.864165 GGATTCTCCGTTCAGATATACAAGTC 59.136 42.308 0.00 0.00 0.00 3.01
9225 9573 5.419760 TCTCCGTTCAGATATACAAGTCG 57.580 43.478 0.00 0.00 0.00 4.18
9226 9574 4.880120 TCTCCGTTCAGATATACAAGTCGT 59.120 41.667 0.00 0.00 0.00 4.34
9227 9575 6.051074 TCTCCGTTCAGATATACAAGTCGTA 58.949 40.000 0.00 0.00 0.00 3.43
9228 9576 6.709397 TCTCCGTTCAGATATACAAGTCGTAT 59.291 38.462 0.00 0.00 43.45 3.06
9229 9577 7.228108 TCTCCGTTCAGATATACAAGTCGTATT 59.772 37.037 0.00 0.00 41.25 1.89
9230 9578 7.709947 TCCGTTCAGATATACAAGTCGTATTT 58.290 34.615 0.00 0.00 41.25 1.40
9231 9579 7.646526 TCCGTTCAGATATACAAGTCGTATTTG 59.353 37.037 0.00 0.00 41.25 2.32
9232 9580 7.646526 CCGTTCAGATATACAAGTCGTATTTGA 59.353 37.037 0.00 0.00 41.25 2.69
9233 9581 8.469902 CGTTCAGATATACAAGTCGTATTTGAC 58.530 37.037 0.00 0.00 41.25 3.18
9234 9582 8.753175 GTTCAGATATACAAGTCGTATTTGACC 58.247 37.037 0.00 0.00 41.25 4.02
9235 9583 7.136772 TCAGATATACAAGTCGTATTTGACCG 58.863 38.462 0.00 0.00 41.25 4.79
9256 9604 2.716217 CCCCAGGTTCAGTCTTTGATC 58.284 52.381 0.00 0.00 35.27 2.92
9280 9628 8.667987 TCGTGTATTTCTTGTGCAAATATTTC 57.332 30.769 0.00 0.00 30.33 2.17
9307 9655 9.632807 GTTAATACTTGCAAATCACAACCATAA 57.367 29.630 0.00 0.00 0.00 1.90
9319 9667 4.220382 TCACAACCATAAGGGAAATGCTTG 59.780 41.667 0.00 0.00 41.15 4.01
9333 9682 1.236616 TGCTTGTGCATCTGAACGGG 61.237 55.000 0.00 0.00 45.31 5.28
9343 9692 0.756294 TCTGAACGGGAAGTGCAAGA 59.244 50.000 0.00 0.00 38.09 3.02
9347 9696 1.673920 GAACGGGAAGTGCAAGAACAA 59.326 47.619 0.00 0.00 0.00 2.83
9363 9712 6.238157 GCAAGAACAATCAATTTGCAAACAGA 60.238 34.615 15.41 15.33 42.63 3.41
9364 9713 6.833342 AGAACAATCAATTTGCAAACAGAC 57.167 33.333 15.41 3.48 39.03 3.51
9365 9714 6.339730 AGAACAATCAATTTGCAAACAGACA 58.660 32.000 15.41 0.00 39.03 3.41
9366 9715 6.477688 AGAACAATCAATTTGCAAACAGACAG 59.522 34.615 15.41 12.79 39.03 3.51
9367 9716 5.904941 ACAATCAATTTGCAAACAGACAGA 58.095 33.333 15.41 6.75 39.03 3.41
9368 9717 5.981315 ACAATCAATTTGCAAACAGACAGAG 59.019 36.000 15.41 8.49 39.03 3.35
9369 9718 4.572985 TCAATTTGCAAACAGACAGAGG 57.427 40.909 15.41 0.00 0.00 3.69
9370 9719 3.318839 TCAATTTGCAAACAGACAGAGGG 59.681 43.478 15.41 0.00 0.00 4.30
9371 9720 1.691196 TTTGCAAACAGACAGAGGGG 58.309 50.000 8.05 0.00 0.00 4.79
9372 9721 0.550914 TTGCAAACAGACAGAGGGGT 59.449 50.000 0.00 0.00 0.00 4.95
9373 9722 0.179020 TGCAAACAGACAGAGGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
9374 9723 0.890996 GCAAACAGACAGAGGGGTGG 60.891 60.000 0.00 0.00 0.00 4.61
9375 9724 0.250901 CAAACAGACAGAGGGGTGGG 60.251 60.000 0.00 0.00 0.00 4.61
9376 9725 1.427072 AAACAGACAGAGGGGTGGGG 61.427 60.000 0.00 0.00 0.00 4.96
9377 9726 3.011517 CAGACAGAGGGGTGGGGG 61.012 72.222 0.00 0.00 0.00 5.40
9401 9750 5.452216 GGGGCTAAAATTGTATTTTACCCGG 60.452 44.000 20.86 0.00 36.79 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 151 2.608090 TCAGCGAGTCAGTAGTACGATG 59.392 50.000 0.00 0.00 40.74 3.84
181 189 9.801873 TGGACATAAACGTTATTTACTAGTACC 57.198 33.333 0.00 0.00 0.00 3.34
184 192 9.933723 AACTGGACATAAACGTTATTTACTAGT 57.066 29.630 0.00 0.00 0.00 2.57
189 197 7.621841 GCGACAACTGGACATAAACGTTATTTA 60.622 37.037 0.00 0.00 0.00 1.40
203 211 3.000080 CTTCGCGCGACAACTGGAC 62.000 63.158 35.02 0.00 0.00 4.02
298 309 1.818674 GGATGGTGGATGTGTTGGTTC 59.181 52.381 0.00 0.00 0.00 3.62
301 312 1.755179 GAGGATGGTGGATGTGTTGG 58.245 55.000 0.00 0.00 0.00 3.77
329 340 1.005037 AAGGATCGCTGTCGTTGCA 60.005 52.632 0.00 0.00 36.96 4.08
381 392 0.622665 AAAGTGGATGAGGGGCTCTG 59.377 55.000 0.00 0.00 0.00 3.35
397 408 3.795488 GCCCCTCAACAGAAAAACGAAAG 60.795 47.826 0.00 0.00 0.00 2.62
403 414 3.677424 CGTTTTGCCCCTCAACAGAAAAA 60.677 43.478 0.00 0.00 33.73 1.94
561 578 2.484889 GGGAGCTTAGGCGTGATTAAG 58.515 52.381 0.00 0.00 44.37 1.85
562 579 1.140252 GGGGAGCTTAGGCGTGATTAA 59.860 52.381 0.00 0.00 44.37 1.40
563 580 0.756903 GGGGAGCTTAGGCGTGATTA 59.243 55.000 0.00 0.00 44.37 1.75
564 581 1.527370 GGGGAGCTTAGGCGTGATT 59.473 57.895 0.00 0.00 44.37 2.57
591 608 0.972883 AGATTAGCGGCCCTGATCTC 59.027 55.000 17.43 1.45 41.57 2.75
685 702 1.286553 AGACTGGTACTCCCCTCTCTG 59.713 57.143 0.00 0.00 0.00 3.35
694 714 1.107945 GGAGCTGGAGACTGGTACTC 58.892 60.000 0.00 0.00 40.30 2.59
735 755 2.372172 GGGGAGAGGACTAGAGAGAGAG 59.628 59.091 0.00 0.00 0.00 3.20
736 756 2.414612 GGGGAGAGGACTAGAGAGAGA 58.585 57.143 0.00 0.00 0.00 3.10
1341 1377 2.362736 CCGCATAAGCCATATCAGCAT 58.637 47.619 0.00 0.00 37.52 3.79
1566 1602 5.050644 CATAACATGCTGAAAGAACTGCA 57.949 39.130 0.00 0.00 45.48 4.41
1729 1766 7.672660 TGAGTAACTCCAGTTAAGATGGACTTA 59.327 37.037 5.41 5.40 41.96 2.24
1730 1767 6.497259 TGAGTAACTCCAGTTAAGATGGACTT 59.503 38.462 5.41 6.17 41.96 3.01
1771 1808 2.777832 ACAATCTCTTGCTCCTGGAC 57.222 50.000 0.00 0.00 35.69 4.02
1972 2009 1.562942 TCCAGAAGGCAGAAGCATCAT 59.437 47.619 0.00 0.00 44.61 2.45
2107 2144 9.734620 TGATTGTGAATCGAATCAATTTTATCC 57.265 29.630 4.38 0.00 40.84 2.59
2281 2325 2.030893 TCTGCACTCTGAATTTTTGCGG 60.031 45.455 0.00 0.00 40.32 5.69
2401 2446 3.437049 GGAAGGCAGAAATATATCCACGC 59.563 47.826 0.00 0.00 0.00 5.34
2684 2740 1.699634 ACCACAACACAGCCTACAGAT 59.300 47.619 0.00 0.00 0.00 2.90
2736 2792 6.012858 TGGATGGTTAAGATAGTTCAGGTTGT 60.013 38.462 0.00 0.00 0.00 3.32
2990 3047 8.082852 CGAGTAATACCCATATGCCTATATGAC 58.917 40.741 8.46 0.00 45.92 3.06
3001 3058 7.070821 ACCAAGACTTTCGAGTAATACCCATAT 59.929 37.037 0.00 0.00 0.00 1.78
3249 3306 9.424319 CAGTGATAAACTTTCTCTTTACAGCTA 57.576 33.333 0.00 0.00 36.83 3.32
3376 3434 1.684248 GCTTCCACCATCCAGCATCTT 60.684 52.381 0.00 0.00 32.17 2.40
3437 3499 4.445718 CGAGATTGATAACTTCACGATGGG 59.554 45.833 0.00 0.00 32.84 4.00
3438 3500 5.281727 TCGAGATTGATAACTTCACGATGG 58.718 41.667 0.00 0.00 32.84 3.51
3441 3503 7.201522 CCAATTTCGAGATTGATAACTTCACGA 60.202 37.037 25.64 0.00 38.93 4.35
3443 3505 7.065803 TCCCAATTTCGAGATTGATAACTTCAC 59.934 37.037 25.64 0.00 38.93 3.18
3455 3517 5.221422 TGCAAACTTTTCCCAATTTCGAGAT 60.221 36.000 0.00 0.00 0.00 2.75
3459 3521 3.494251 CCTGCAAACTTTTCCCAATTTCG 59.506 43.478 0.00 0.00 0.00 3.46
3492 3554 2.595380 ACCCACCCTCCTAATTCCTAGA 59.405 50.000 0.00 0.00 0.00 2.43
3493 3555 2.973406 GACCCACCCTCCTAATTCCTAG 59.027 54.545 0.00 0.00 0.00 3.02
3520 3582 4.823442 TCATATCTCAATGCGCTCCAATTT 59.177 37.500 9.73 0.00 0.00 1.82
3584 3697 3.508793 ACACCATTCATCAAGAAAGGCAG 59.491 43.478 0.00 0.00 46.56 4.85
3865 3981 3.981211 ACATCAACTGAATGTTGGTTGC 58.019 40.909 8.39 0.00 46.94 4.17
4160 4276 0.107456 CACTGACACTGCTCCACCTT 59.893 55.000 0.00 0.00 0.00 3.50
4313 4429 0.613260 TGTCTGGATTCTTCACCCCG 59.387 55.000 0.00 0.00 0.00 5.73
4361 4477 0.609131 AATCCTTGGGCTTGTCACCG 60.609 55.000 0.00 0.00 0.00 4.94
4419 4535 4.284490 TGATAATGAGGGTGGAGATGTAGC 59.716 45.833 0.00 0.00 0.00 3.58
4455 4571 1.423161 AGTCTGCTTTTCAGGAGCCTT 59.577 47.619 0.00 0.00 43.06 4.35
4575 4691 0.110056 GCAACATGCTCTGACAACCG 60.110 55.000 0.00 0.00 40.96 4.44
4666 4782 9.653287 CTGACAATGGACTAGTTAAAGTATCAA 57.347 33.333 0.00 0.00 0.00 2.57
4877 4996 3.673902 TGTGGCTTTCGATTTGAGATCA 58.326 40.909 0.00 0.00 0.00 2.92
4889 5008 1.267732 CGAGAATGCGATGTGGCTTTC 60.268 52.381 7.30 7.30 43.52 2.62
4901 5020 3.248602 CCCTAACATTAGTGCGAGAATGC 59.751 47.826 4.65 0.00 36.67 3.56
4902 5021 3.809832 CCCCTAACATTAGTGCGAGAATG 59.190 47.826 0.00 3.48 38.70 2.67
5059 5178 2.632996 CCCTGGCGACTAGAATAATCCA 59.367 50.000 0.00 0.00 0.00 3.41
5262 5381 4.545610 GTTAGCTTGTGTGCAGCAAATAA 58.454 39.130 0.00 0.00 34.99 1.40
5327 5446 6.071165 GCTTTACCTCACTTAACCTAGGTGTA 60.071 42.308 17.14 7.77 42.31 2.90
5782 5901 1.826385 ACAGAGTACAGCATTTGGGC 58.174 50.000 0.00 0.00 0.00 5.36
6279 6398 2.960384 ACTACGGGAAAAACCTTTTGGG 59.040 45.455 0.00 0.00 46.08 4.12
6334 6453 4.726317 TGACCCCCTTGATTGATCTTGATA 59.274 41.667 0.00 0.00 0.00 2.15
6747 6866 1.334689 GCTTCCCGTGGAAAAGAAACG 60.335 52.381 6.79 0.00 41.54 3.60
7384 7503 3.920817 TGTCATGGGGGACAAGCT 58.079 55.556 0.00 0.00 44.34 3.74
7485 7604 2.821969 CTGGAAACATGAAGGACCCTTG 59.178 50.000 5.96 0.00 41.51 3.61
7486 7605 2.716424 TCTGGAAACATGAAGGACCCTT 59.284 45.455 0.00 0.04 41.51 3.95
7520 7665 7.253750 CAAATAGTTTGACTTCACACAAAGTGC 60.254 37.037 0.00 0.00 44.37 4.40
7639 7784 8.178313 GCTTTTCAGCAAGGATAAAGTAACTAG 58.822 37.037 0.00 0.00 46.49 2.57
7640 7785 8.040716 GCTTTTCAGCAAGGATAAAGTAACTA 57.959 34.615 0.00 0.00 46.49 2.24
7698 7843 6.097412 AGGATAGAAACAATTGATTCCAAGGC 59.903 38.462 20.98 9.29 35.48 4.35
7721 7866 6.771749 AGAGATAGAAGCAATTGATTCCAAGG 59.228 38.462 27.97 0.00 41.02 3.61
7722 7867 7.804843 AGAGATAGAAGCAATTGATTCCAAG 57.195 36.000 27.97 0.00 41.02 3.61
7723 7868 7.830697 TCAAGAGATAGAAGCAATTGATTCCAA 59.169 33.333 27.97 18.98 41.02 3.53
7724 7869 7.281774 GTCAAGAGATAGAAGCAATTGATTCCA 59.718 37.037 27.97 18.41 41.02 3.53
7725 7870 7.281774 TGTCAAGAGATAGAAGCAATTGATTCC 59.718 37.037 27.97 15.74 41.02 3.01
7726 7871 8.206325 TGTCAAGAGATAGAAGCAATTGATTC 57.794 34.615 25.27 25.27 40.47 2.52
7727 7872 8.622157 CATGTCAAGAGATAGAAGCAATTGATT 58.378 33.333 9.03 9.03 0.00 2.57
7728 7873 7.991460 TCATGTCAAGAGATAGAAGCAATTGAT 59.009 33.333 10.34 0.00 0.00 2.57
7729 7874 7.333323 TCATGTCAAGAGATAGAAGCAATTGA 58.667 34.615 10.34 0.00 0.00 2.57
7730 7875 7.549615 TCATGTCAAGAGATAGAAGCAATTG 57.450 36.000 0.00 0.00 0.00 2.32
7731 7876 8.622157 CATTCATGTCAAGAGATAGAAGCAATT 58.378 33.333 0.00 0.00 0.00 2.32
7732 7877 7.774157 ACATTCATGTCAAGAGATAGAAGCAAT 59.226 33.333 0.00 0.00 35.87 3.56
7733 7878 7.108194 ACATTCATGTCAAGAGATAGAAGCAA 58.892 34.615 0.00 0.00 35.87 3.91
7734 7879 6.647229 ACATTCATGTCAAGAGATAGAAGCA 58.353 36.000 0.00 0.00 35.87 3.91
7735 7880 8.830201 ATACATTCATGTCAAGAGATAGAAGC 57.170 34.615 0.00 0.00 41.97 3.86
7736 7881 9.127006 CGATACATTCATGTCAAGAGATAGAAG 57.873 37.037 0.00 0.00 41.97 2.85
7737 7882 8.633561 ACGATACATTCATGTCAAGAGATAGAA 58.366 33.333 0.00 0.00 41.97 2.10
7738 7883 8.171164 ACGATACATTCATGTCAAGAGATAGA 57.829 34.615 0.00 0.00 41.97 1.98
7739 7884 8.809159 AACGATACATTCATGTCAAGAGATAG 57.191 34.615 0.00 0.00 41.97 2.08
7740 7885 9.034544 CAAACGATACATTCATGTCAAGAGATA 57.965 33.333 0.00 0.00 41.97 1.98
7741 7886 7.466455 GCAAACGATACATTCATGTCAAGAGAT 60.466 37.037 0.00 0.00 41.97 2.75
7742 7887 6.183360 GCAAACGATACATTCATGTCAAGAGA 60.183 38.462 0.00 0.00 41.97 3.10
7841 7986 0.704664 AGGGAGTTGGAATTGGGGAC 59.295 55.000 0.00 0.00 0.00 4.46
7903 8048 1.675641 GGTCCACCCATGTCACTGC 60.676 63.158 0.00 0.00 0.00 4.40
8059 8204 4.636249 ACAGTAACTGAAGCCTGAAAGAG 58.364 43.478 0.00 0.00 33.00 2.85
8266 8442 4.260784 GGGTTATGTTCTAATTGAGCAGCG 60.261 45.833 0.00 0.00 39.21 5.18
8392 8568 1.087501 GGGAGAAGAATGAACGTGGC 58.912 55.000 0.00 0.00 0.00 5.01
8525 8702 1.525718 TAGCAGTGTCCGCGTACCAA 61.526 55.000 4.92 0.00 0.00 3.67
8676 8854 7.538303 AAATTGCAACAACAAAAGTTCTAGG 57.462 32.000 0.00 0.00 32.27 3.02
8682 8860 6.206438 AGTGGAAAAATTGCAACAACAAAAGT 59.794 30.769 0.00 0.00 32.27 2.66
8683 8861 6.610456 AGTGGAAAAATTGCAACAACAAAAG 58.390 32.000 0.00 0.00 32.27 2.27
8797 8975 5.929992 CACAGCTTTGAAATGGATTTGTGAT 59.070 36.000 0.00 0.00 0.00 3.06
8798 8976 5.163426 ACACAGCTTTGAAATGGATTTGTGA 60.163 36.000 6.92 0.00 0.00 3.58
8906 9084 0.252375 GGGGCCCCATTATGCATCAT 60.252 55.000 37.61 0.00 35.81 2.45
8995 9298 5.611796 TCCAAGAATTCTGACACGAATTG 57.388 39.130 9.17 0.00 42.09 2.32
9050 9353 0.452987 CATGGGGAGTTTGCATGTCG 59.547 55.000 0.00 0.00 0.00 4.35
9107 9438 7.719633 TGCCTCTTATTTACAAGTTCTTGAAGT 59.280 33.333 17.75 8.14 0.00 3.01
9171 9519 2.920724 TTTTGATGGAGACGTGGTCA 57.079 45.000 0.00 0.00 34.60 4.02
9207 9555 8.469902 GTCAAATACGACTTGTATATCTGAACG 58.530 37.037 0.00 0.00 43.04 3.95
9220 9568 0.392060 GGGGCGGTCAAATACGACTT 60.392 55.000 0.00 0.00 38.41 3.01
9221 9569 1.219935 GGGGCGGTCAAATACGACT 59.780 57.895 0.00 0.00 38.41 4.18
9222 9570 1.078988 TGGGGCGGTCAAATACGAC 60.079 57.895 0.00 0.00 37.40 4.34
9223 9571 1.219664 CTGGGGCGGTCAAATACGA 59.780 57.895 0.00 0.00 0.00 3.43
9224 9572 1.817941 CCTGGGGCGGTCAAATACG 60.818 63.158 0.00 0.00 0.00 3.06
9225 9573 0.323087 AACCTGGGGCGGTCAAATAC 60.323 55.000 0.00 0.00 35.89 1.89
9226 9574 0.034863 GAACCTGGGGCGGTCAAATA 60.035 55.000 0.00 0.00 35.89 1.40
9227 9575 1.304134 GAACCTGGGGCGGTCAAAT 60.304 57.895 0.00 0.00 35.89 2.32
9228 9576 2.114411 GAACCTGGGGCGGTCAAA 59.886 61.111 0.00 0.00 35.89 2.69
9229 9577 3.172106 TGAACCTGGGGCGGTCAA 61.172 61.111 0.00 0.00 35.89 3.18
9230 9578 3.636231 CTGAACCTGGGGCGGTCA 61.636 66.667 0.00 0.00 35.89 4.02
9231 9579 3.607370 GACTGAACCTGGGGCGGTC 62.607 68.421 12.31 12.31 35.89 4.79
9232 9580 3.637273 GACTGAACCTGGGGCGGT 61.637 66.667 0.00 0.00 39.48 5.68
9233 9581 2.411765 AAAGACTGAACCTGGGGCGG 62.412 60.000 0.00 0.00 0.00 6.13
9234 9582 1.073199 AAAGACTGAACCTGGGGCG 59.927 57.895 0.00 0.00 0.00 6.13
9235 9583 0.110486 TCAAAGACTGAACCTGGGGC 59.890 55.000 0.00 0.00 0.00 5.80
9256 9604 7.270365 ACGAAATATTTGCACAAGAAATACACG 59.730 33.333 5.17 0.00 30.08 4.49
9280 9628 6.146216 TGGTTGTGATTTGCAAGTATTAACG 58.854 36.000 0.00 0.00 0.00 3.18
9285 9633 6.127366 CCCTTATGGTTGTGATTTGCAAGTAT 60.127 38.462 0.00 0.00 0.00 2.12
9291 9639 4.799564 TTCCCTTATGGTTGTGATTTGC 57.200 40.909 0.00 0.00 34.77 3.68
9319 9667 0.798776 CACTTCCCGTTCAGATGCAC 59.201 55.000 0.00 0.00 0.00 4.57
9328 9677 1.757682 TTGTTCTTGCACTTCCCGTT 58.242 45.000 0.00 0.00 0.00 4.44
9333 9682 5.234757 TGCAAATTGATTGTTCTTGCACTTC 59.765 36.000 0.00 0.00 45.38 3.01
9343 9692 6.339730 TCTGTCTGTTTGCAAATTGATTGTT 58.660 32.000 16.21 0.00 41.32 2.83
9347 9696 4.021719 CCCTCTGTCTGTTTGCAAATTGAT 60.022 41.667 16.21 0.00 0.00 2.57
9380 9729 5.045215 GCCCGGGTAAAATACAATTTTAGC 58.955 41.667 24.63 18.96 39.98 3.09
9381 9730 6.210287 TGCCCGGGTAAAATACAATTTTAG 57.790 37.500 24.63 0.00 0.00 1.85
9382 9731 6.210984 ACTTGCCCGGGTAAAATACAATTTTA 59.789 34.615 25.04 0.00 0.00 1.52
9383 9732 5.012251 ACTTGCCCGGGTAAAATACAATTTT 59.988 36.000 25.04 2.29 0.00 1.82
9384 9733 4.528987 ACTTGCCCGGGTAAAATACAATTT 59.471 37.500 25.04 4.61 0.00 1.82
9385 9734 4.090819 ACTTGCCCGGGTAAAATACAATT 58.909 39.130 25.04 8.47 0.00 2.32
9386 9735 3.703921 ACTTGCCCGGGTAAAATACAAT 58.296 40.909 25.04 4.99 0.00 2.71
9387 9736 3.157750 ACTTGCCCGGGTAAAATACAA 57.842 42.857 25.04 15.42 0.00 2.41
9388 9737 2.883122 ACTTGCCCGGGTAAAATACA 57.117 45.000 25.04 8.11 0.00 2.29
9389 9738 5.584442 CATTTACTTGCCCGGGTAAAATAC 58.416 41.667 25.04 5.19 40.00 1.89
9390 9739 4.098196 GCATTTACTTGCCCGGGTAAAATA 59.902 41.667 25.04 16.75 40.00 1.40
9391 9740 3.118920 GCATTTACTTGCCCGGGTAAAAT 60.119 43.478 25.04 18.12 40.00 1.82
9392 9741 2.231721 GCATTTACTTGCCCGGGTAAAA 59.768 45.455 25.04 16.63 40.00 1.52
9393 9742 1.819903 GCATTTACTTGCCCGGGTAAA 59.180 47.619 25.04 19.20 40.57 2.01
9394 9743 1.271982 TGCATTTACTTGCCCGGGTAA 60.272 47.619 23.61 23.61 42.06 2.85
9395 9744 0.328592 TGCATTTACTTGCCCGGGTA 59.671 50.000 24.63 16.91 42.06 3.69
9396 9745 0.540830 TTGCATTTACTTGCCCGGGT 60.541 50.000 24.63 4.02 42.06 5.28
9401 9750 6.973229 AGAATTTGATTGCATTTACTTGCC 57.027 33.333 0.00 0.00 42.06 4.52



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

AutoCloner maintained by Alex Coulton.