Multiple sequence alignment - TraesCS3B01G202800

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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 TraesCS3B01G202800 chr3B 100.000 6178 0 0 1 6178 237105299 237111476 0.000000e+00 11409.0
1 TraesCS3B01G202800 chr3D 95.882 6193 144 36 1 6146 160555566 160561694 0.000000e+00 9921.0
2 TraesCS3B01G202800 chr3A 95.843 5004 103 38 601 5568 186745522 186750456 0.000000e+00 7991.0
3 TraesCS3B01G202800 chr3A 95.329 835 31 6 3123 3951 740075080 740074248 0.000000e+00 1319.0
4 TraesCS3B01G202800 chr3A 95.310 597 28 0 1 597 186730409 186731005 0.000000e+00 948.0
5 TraesCS3B01G202800 chr3A 91.188 522 21 3 5625 6146 186750452 186750948 0.000000e+00 686.0
6 TraesCS3B01G202800 chr7D 94.724 815 35 7 3123 3931 478676378 478675566 0.000000e+00 1260.0
7 TraesCS3B01G202800 chr7D 100.000 31 0 0 4074 4104 140234087 140234117 2.410000e-04 58.4
8 TraesCS3B01G202800 chrUn 93.632 424 13 8 3532 3951 11557360 11556947 6.800000e-174 621.0
9 TraesCS3B01G202800 chrUn 96.078 255 8 1 3123 3375 11557619 11557365 1.240000e-111 414.0
10 TraesCS3B01G202800 chr7B 94.737 380 14 5 3576 3951 173307737 173307360 2.480000e-163 586.0
11 TraesCS3B01G202800 chr2D 92.750 400 25 3 3123 3520 302988646 302988249 5.370000e-160 575.0
12 TraesCS3B01G202800 chr4B 92.199 282 18 2 3242 3520 220391017 220390737 4.490000e-106 396.0
13 TraesCS3B01G202800 chr4B 92.647 136 7 2 3123 3255 220392572 220392437 6.320000e-45 193.0
14 TraesCS3B01G202800 chr4A 88.776 98 9 1 2973 3070 65140897 65140992 1.090000e-22 119.0


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 TraesCS3B01G202800 chr3B 237105299 237111476 6177 False 11409.0 11409 100.0000 1 6178 1 chr3B.!!$F1 6177
1 TraesCS3B01G202800 chr3D 160555566 160561694 6128 False 9921.0 9921 95.8820 1 6146 1 chr3D.!!$F1 6145
2 TraesCS3B01G202800 chr3A 186745522 186750948 5426 False 4338.5 7991 93.5155 601 6146 2 chr3A.!!$F2 5545
3 TraesCS3B01G202800 chr3A 740074248 740075080 832 True 1319.0 1319 95.3290 3123 3951 1 chr3A.!!$R1 828
4 TraesCS3B01G202800 chr3A 186730409 186731005 596 False 948.0 948 95.3100 1 597 1 chr3A.!!$F1 596
5 TraesCS3B01G202800 chr7D 478675566 478676378 812 True 1260.0 1260 94.7240 3123 3931 1 chr7D.!!$R1 808
6 TraesCS3B01G202800 chrUn 11556947 11557619 672 True 517.5 621 94.8550 3123 3951 2 chrUn.!!$R1 828
7 TraesCS3B01G202800 chr4B 220390737 220392572 1835 True 294.5 396 92.4230 3123 3520 2 chr4B.!!$R1 397

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
726 730 0.184933 CGGGCCCAATAAATCAGGGA 59.815 55.000 24.92 0.0 45.80 4.20 F
1226 1241 0.987294 ATACTGCACACTTCTGCCCT 59.013 50.000 0.00 0.0 36.21 5.19 F
1605 1636 1.471676 CCAGCCTTATGACTCGTCACC 60.472 57.143 1.26 0.0 43.11 4.02 F
2508 2542 0.598065 ACCTTGTTCTCGCAAATGGC 59.402 50.000 0.00 0.0 39.90 4.40 F
3822 5306 1.271871 TGTTCATTGTGGCTAGTGGGG 60.272 52.381 0.00 0.0 0.00 4.96 F
4729 6214 0.815615 GGGCAACTATGGAAGCTCCG 60.816 60.000 0.00 0.0 40.17 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1613 0.108138 ACGAGTCATAAGGCTGGTGC 60.108 55.000 0.00 0.0 38.76 5.01 R
2096 2129 1.002857 CCTGGAGTTGGGGGAAATCT 58.997 55.000 0.00 0.0 0.00 2.40 R
3375 4851 2.620115 AGTGTGATCACAAAGCAGGTTG 59.380 45.455 29.42 0.0 46.01 3.77 R
4224 5709 1.600638 CAGCAGATGCACCAGAGGA 59.399 57.895 7.68 0.0 45.16 3.71 R
4778 6263 0.179073 CCGACCTGTATTCAGCCCAG 60.179 60.000 0.00 0.0 40.09 4.45 R
6031 7529 0.113580 TCATGATCGGGATCGGGGTA 59.886 55.000 4.36 0.0 40.63 3.69 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
48 49 6.481976 ACGCCATTCGAAGATAAATTCACATA 59.518 34.615 3.35 0.00 41.67 2.29
69 70 9.605275 CACATAAAATGAACTCCTCAGATCTTA 57.395 33.333 0.00 0.00 37.52 2.10
79 80 7.309770 ACTCCTCAGATCTTACTTCAACTTT 57.690 36.000 0.00 0.00 0.00 2.66
95 96 5.214417 TCAACTTTCTTGATCATTGCGTTG 58.786 37.500 14.25 14.25 0.00 4.10
126 127 5.773680 CCCTTTGATCCATGCTTTATCTCAT 59.226 40.000 0.00 0.00 0.00 2.90
269 270 2.099098 CCATTGCCGAGGAACCATAAAC 59.901 50.000 0.00 0.00 0.00 2.01
298 299 2.215196 GTGGTCTTTACAAACTGGCGA 58.785 47.619 0.00 0.00 0.00 5.54
309 310 2.587194 CTGGCGATGAAGCTCCCG 60.587 66.667 0.00 0.00 37.29 5.14
368 369 3.528370 CCACTCCTACTCCCGGCG 61.528 72.222 0.00 0.00 0.00 6.46
383 384 1.082117 CGGCGTCTTCCACACATACC 61.082 60.000 0.00 0.00 0.00 2.73
385 386 1.082117 GCGTCTTCCACACATACCCG 61.082 60.000 0.00 0.00 0.00 5.28
463 464 0.960364 GGATTGTTTCGAGCCCAGCA 60.960 55.000 0.00 0.00 0.00 4.41
506 507 1.148048 GGGCTCTGCAGGATTCCTC 59.852 63.158 15.13 0.00 0.00 3.71
560 561 2.561569 CCAACGGGTTACCATCATCTC 58.438 52.381 2.98 0.00 36.13 2.75
597 598 0.613260 GTGGCATGACACCTACTCCA 59.387 55.000 21.83 0.00 35.34 3.86
611 615 8.235359 ACACCTACTCCATATAGAGTACAAAC 57.765 38.462 6.90 0.00 45.31 2.93
631 635 6.882140 ACAAACAATCCATAGTCGGACAAATA 59.118 34.615 11.27 0.00 38.07 1.40
632 636 7.392113 ACAAACAATCCATAGTCGGACAAATAA 59.608 33.333 11.27 0.00 38.07 1.40
633 637 7.931578 AACAATCCATAGTCGGACAAATAAA 57.068 32.000 11.27 0.00 38.07 1.40
634 638 8.519799 AACAATCCATAGTCGGACAAATAAAT 57.480 30.769 11.27 0.00 38.07 1.40
722 726 3.054287 TCAGTAACGGGCCCAATAAATCA 60.054 43.478 24.92 0.00 0.00 2.57
726 730 0.184933 CGGGCCCAATAAATCAGGGA 59.815 55.000 24.92 0.00 45.80 4.20
906 921 4.761304 TCTCCCCTCCCCTCCCCT 62.761 72.222 0.00 0.00 0.00 4.79
1179 1194 3.253061 GCCCAGGCTCCTATCCCC 61.253 72.222 0.08 0.00 38.26 4.81
1226 1241 0.987294 ATACTGCACACTTCTGCCCT 59.013 50.000 0.00 0.00 36.21 5.19
1273 1290 2.235898 AGTGCTTCTGGAGTCTGAATCC 59.764 50.000 16.82 16.82 37.35 3.01
1305 1336 3.162666 ACACGAGGTTCCAGATGAGTTA 58.837 45.455 0.00 0.00 0.00 2.24
1539 1570 4.220602 GCCAGATTAGTTGGTGGTTTGATT 59.779 41.667 0.00 0.00 38.02 2.57
1602 1633 1.927895 CACCAGCCTTATGACTCGTC 58.072 55.000 0.00 0.00 0.00 4.20
1605 1636 1.471676 CCAGCCTTATGACTCGTCACC 60.472 57.143 1.26 0.00 43.11 4.02
1606 1637 1.478510 CAGCCTTATGACTCGTCACCT 59.521 52.381 1.26 0.00 43.11 4.00
1720 1753 5.070847 AGTTTTCATTTGATTTGGGTGCTCT 59.929 36.000 0.00 0.00 0.00 4.09
1750 1783 6.385649 TGCCAAAACTACCTTTGTTTAGAG 57.614 37.500 0.00 0.00 36.72 2.43
1756 1789 5.291905 ACTACCTTTGTTTAGAGCAGTGT 57.708 39.130 0.00 0.00 0.00 3.55
1777 1810 2.669364 GCTGTTTGCAGACCTTTCATG 58.331 47.619 4.73 0.00 45.28 3.07
1782 1815 1.538047 TGCAGACCTTTCATGGCTTC 58.462 50.000 0.00 0.00 0.00 3.86
2096 2129 7.116376 CGATTTGTGCAGTTTCTTACTAGAGAA 59.884 37.037 0.00 0.00 34.56 2.87
2118 2151 2.366153 TTTCCCCCAACTCCAGGTGC 62.366 60.000 0.00 0.00 0.00 5.01
2149 2182 6.043411 ACGGACTCTTATTCTTGTAATCTGC 58.957 40.000 0.00 0.00 0.00 4.26
2150 2183 6.127310 ACGGACTCTTATTCTTGTAATCTGCT 60.127 38.462 0.00 0.00 0.00 4.24
2180 2213 6.066690 GGACCCTTACCAACTAAACTTCTTT 58.933 40.000 0.00 0.00 0.00 2.52
2397 2431 3.766591 TGTCCTGGTTGAATGTTTGTTGT 59.233 39.130 0.00 0.00 0.00 3.32
2398 2432 4.221703 TGTCCTGGTTGAATGTTTGTTGTT 59.778 37.500 0.00 0.00 0.00 2.83
2399 2433 4.566360 GTCCTGGTTGAATGTTTGTTGTTG 59.434 41.667 0.00 0.00 0.00 3.33
2496 2530 1.822186 AAAGTGCCGCGACCTTGTT 60.822 52.632 8.23 0.00 0.00 2.83
2508 2542 0.598065 ACCTTGTTCTCGCAAATGGC 59.402 50.000 0.00 0.00 39.90 4.40
2638 2672 8.246180 CAGCATTTGATCAGGTTTTATACACTT 58.754 33.333 0.00 0.00 0.00 3.16
2645 2679 8.243426 TGATCAGGTTTTATACACTTTTGCATC 58.757 33.333 0.00 0.00 0.00 3.91
2648 2682 9.461312 TCAGGTTTTATACACTTTTGCATCTAT 57.539 29.630 0.00 0.00 0.00 1.98
2679 2713 5.853936 TGTGATTAGTAGTCAACAGCAGTT 58.146 37.500 0.00 0.00 38.88 3.16
2680 2714 6.988522 TGTGATTAGTAGTCAACAGCAGTTA 58.011 36.000 0.00 0.00 35.85 2.24
2681 2715 6.866770 TGTGATTAGTAGTCAACAGCAGTTAC 59.133 38.462 0.00 0.00 35.85 2.50
2682 2716 7.091443 GTGATTAGTAGTCAACAGCAGTTACT 58.909 38.462 0.00 0.00 35.85 2.24
2890 2928 3.009033 TCTCCTGTATGTTTCAACCCTGG 59.991 47.826 0.00 0.00 0.00 4.45
2910 2948 5.305644 CCTGGGTTACAACTCTCTGCTATAT 59.694 44.000 0.00 0.00 0.00 0.86
3083 3121 9.233232 GTAACTCATTCATTTTCGTTTTGTTCT 57.767 29.630 0.00 0.00 0.00 3.01
3292 4768 4.756642 TCTGATAGTTTGGTTGCTCACTTG 59.243 41.667 0.00 0.00 0.00 3.16
3301 4777 3.060602 GGTTGCTCACTTGACTACACTC 58.939 50.000 0.00 0.00 0.00 3.51
3315 4791 3.971971 ACTACACTCTTACCCCAACAGTT 59.028 43.478 0.00 0.00 0.00 3.16
3356 4832 7.981102 AGTCTGTTTCCCTATTCAAGTAAAC 57.019 36.000 0.00 0.00 33.17 2.01
3375 4851 4.531659 AACTGCTCGTCAAGTTTTACAC 57.468 40.909 0.00 0.00 0.00 2.90
3377 4853 3.936453 ACTGCTCGTCAAGTTTTACACAA 59.064 39.130 0.00 0.00 0.00 3.33
3460 4939 5.986936 TCGTATCTGTGATTACTAGCTTCG 58.013 41.667 0.00 0.00 0.00 3.79
3468 4947 7.499563 TCTGTGATTACTAGCTTCGTTAGAGAT 59.500 37.037 0.00 0.00 0.00 2.75
3515 4995 7.966246 TTTCCGTGTTATTAAGCTTGTCTTA 57.034 32.000 9.86 0.00 36.25 2.10
3662 5142 5.652891 ACAAAGATCAGATACAGGTACGAGT 59.347 40.000 0.00 0.00 0.00 4.18
3698 5178 7.397221 TCTCACATGGTTTCTTCTCATGTTAT 58.603 34.615 5.56 0.00 46.20 1.89
3699 5179 7.335171 TCTCACATGGTTTCTTCTCATGTTATG 59.665 37.037 5.56 0.00 46.20 1.90
3822 5306 1.271871 TGTTCATTGTGGCTAGTGGGG 60.272 52.381 0.00 0.00 0.00 4.96
3863 5347 9.104965 TGTTATCAATATGCTAGTGGTACAAAC 57.895 33.333 0.00 0.00 44.16 2.93
3878 5362 1.611491 ACAAACAACTAATGCCGGTGG 59.389 47.619 1.90 0.00 0.00 4.61
3948 5433 7.064728 GGTTCAACTAGATGTAAATGACAGTCC 59.935 40.741 0.00 0.00 42.79 3.85
4086 5571 5.535406 ACATAATGAGTTACTCCCTCCGTAG 59.465 44.000 10.10 0.00 0.00 3.51
4100 5585 6.850234 TCCCTCCGTAGAGAAATATAAGAGT 58.150 40.000 0.00 0.00 43.39 3.24
4131 5616 7.623999 AGGATCCATGTATTAGTCATCAAGT 57.376 36.000 15.82 0.00 0.00 3.16
4224 5709 6.186957 TGTGATTACTGCTGGAATTATTGGT 58.813 36.000 2.17 0.00 0.00 3.67
4339 5824 7.148407 ACGACCAAATCAAGTATGTTCTCATTC 60.148 37.037 0.00 0.00 35.70 2.67
4340 5825 7.148423 CGACCAAATCAAGTATGTTCTCATTCA 60.148 37.037 0.00 0.00 35.70 2.57
4365 5850 9.577110 CACTGTTATTCAGATTACATGCAAATT 57.423 29.630 0.00 0.00 46.27 1.82
4567 6052 4.432741 GGTGCTTCTGGGGAGGGC 62.433 72.222 0.00 0.00 0.00 5.19
4672 6157 4.630644 TGAGAAGGCTGTGAAGATTCTT 57.369 40.909 0.00 0.00 30.62 2.52
4729 6214 0.815615 GGGCAACTATGGAAGCTCCG 60.816 60.000 0.00 0.00 40.17 4.63
4778 6263 0.038166 TGGCAACCCTGATCTGAACC 59.962 55.000 0.38 0.00 0.00 3.62
4956 6441 2.253452 CCTTGTCGCTGCAGTTGC 59.747 61.111 16.64 0.05 42.50 4.17
5302 6792 4.556942 TGTCAATGTCAGCTTTCACTTG 57.443 40.909 0.00 0.00 0.00 3.16
5339 6829 3.098636 GTGTCGTTGCTCAGTTTTGTTC 58.901 45.455 0.00 0.00 0.00 3.18
5341 6831 3.063452 TGTCGTTGCTCAGTTTTGTTCTC 59.937 43.478 0.00 0.00 0.00 2.87
5370 6860 8.167605 TCAATTTTGATTTGCATGTTCCAATT 57.832 26.923 0.00 0.00 31.01 2.32
5422 6912 3.431207 GCAGGCCAAATGAACAGCATAAT 60.431 43.478 5.01 0.00 35.78 1.28
5499 6989 7.977789 TCAGCGAATAATAATCCAATTGCTA 57.022 32.000 0.00 0.00 0.00 3.49
5500 6990 7.806690 TCAGCGAATAATAATCCAATTGCTAC 58.193 34.615 0.00 0.00 0.00 3.58
5501 6991 7.661437 TCAGCGAATAATAATCCAATTGCTACT 59.339 33.333 0.00 0.00 0.00 2.57
5502 6992 8.292448 CAGCGAATAATAATCCAATTGCTACTT 58.708 33.333 0.00 0.00 0.00 2.24
5503 6993 9.502091 AGCGAATAATAATCCAATTGCTACTTA 57.498 29.630 0.00 0.00 0.00 2.24
5557 7047 5.525199 ACGAAAAGGAATTTTACGTGCATT 58.475 33.333 0.00 0.00 31.66 3.56
5566 7056 2.455674 TTACGTGCATTGTCTCTGCT 57.544 45.000 0.00 0.00 40.34 4.24
5570 7060 1.128136 CGTGCATTGTCTCTGCTCTTG 59.872 52.381 0.00 0.00 40.34 3.02
5586 7076 3.751621 CTCTTGTTCGACCATTCATTGC 58.248 45.455 0.00 0.00 0.00 3.56
5598 7088 1.825090 TTCATTGCGTCAGGCTCATT 58.175 45.000 0.00 0.00 44.05 2.57
5636 7128 4.476628 CCATTCATTGGCTTAGGCTTTT 57.523 40.909 7.43 0.00 39.09 2.27
5689 7187 2.661537 CACGCGTTGCTGGACTGA 60.662 61.111 10.22 0.00 0.00 3.41
5698 7196 1.228245 GCTGGACTGAACCTGGCAA 60.228 57.895 0.00 0.00 32.92 4.52
5802 7300 2.670934 CAGGTGGTGCTGCTGGAC 60.671 66.667 6.70 6.70 0.00 4.02
5803 7301 4.320456 AGGTGGTGCTGCTGGACG 62.320 66.667 9.05 0.00 35.23 4.79
5813 7311 4.910585 GCTGGACGCCGGGGTATG 62.911 72.222 25.76 17.41 0.00 2.39
5814 7312 4.235762 CTGGACGCCGGGGTATGG 62.236 72.222 25.76 12.93 0.00 2.74
5816 7314 4.540735 GGACGCCGGGGTATGGTG 62.541 72.222 25.76 0.00 42.74 4.17
6031 7529 3.374402 CTGACGTGGCCGGACTCT 61.374 66.667 9.82 0.00 38.78 3.24
6093 7591 0.734889 CAAATCCTGCACCCATCGAC 59.265 55.000 0.00 0.00 0.00 4.20
6094 7592 0.744414 AAATCCTGCACCCATCGACG 60.744 55.000 0.00 0.00 0.00 5.12
6100 7598 2.094659 GCACCCATCGACGAGTGTG 61.095 63.158 14.75 15.27 32.75 3.82
6101 7599 2.094659 CACCCATCGACGAGTGTGC 61.095 63.158 3.01 0.00 0.00 4.57
6102 7600 2.276116 ACCCATCGACGAGTGTGCT 61.276 57.895 3.01 0.00 0.00 4.40
6103 7601 1.517257 CCCATCGACGAGTGTGCTC 60.517 63.158 3.01 0.00 38.35 4.26
6111 7609 5.244785 TCGACGAGTGTGCTCTTATTATT 57.755 39.130 0.00 0.00 39.53 1.40
6123 7621 7.282224 TGTGCTCTTATTATTAATCCACACCAC 59.718 37.037 0.00 0.00 0.00 4.16
6126 7624 7.448469 GCTCTTATTATTAATCCACACCACCAT 59.552 37.037 0.00 0.00 0.00 3.55
6127 7625 9.354673 CTCTTATTATTAATCCACACCACCATT 57.645 33.333 0.00 0.00 0.00 3.16
6128 7626 9.349713 TCTTATTATTAATCCACACCACCATTC 57.650 33.333 0.00 0.00 0.00 2.67
6129 7627 9.354673 CTTATTATTAATCCACACCACCATTCT 57.645 33.333 0.00 0.00 0.00 2.40
6157 7655 2.572812 TGCATGGCATGGTTTCGC 59.427 55.556 27.48 13.38 31.71 4.70
6158 7656 2.580326 GCATGGCATGGTTTCGCG 60.580 61.111 27.48 0.00 0.00 5.87
6159 7657 2.102749 CATGGCATGGTTTCGCGG 59.897 61.111 19.80 0.00 0.00 6.46
6160 7658 3.825611 ATGGCATGGTTTCGCGGC 61.826 61.111 6.13 0.00 0.00 6.53
6164 7662 4.101790 CATGGTTTCGCGGCGCTT 62.102 61.111 30.54 2.55 0.00 4.68
6165 7663 4.101790 ATGGTTTCGCGGCGCTTG 62.102 61.111 30.54 15.69 0.00 4.01
6167 7665 4.020378 GGTTTCGCGGCGCTTGAA 62.020 61.111 30.54 22.86 0.00 2.69
6168 7666 2.051703 GTTTCGCGGCGCTTGAAA 60.052 55.556 30.54 26.92 0.00 2.69
6169 7667 2.074920 GTTTCGCGGCGCTTGAAAG 61.075 57.895 30.54 13.27 32.70 2.62
6170 7668 2.539338 TTTCGCGGCGCTTGAAAGT 61.539 52.632 30.54 0.00 0.00 2.66
6171 7669 1.222766 TTTCGCGGCGCTTGAAAGTA 61.223 50.000 30.54 9.12 0.00 2.24
6172 7670 1.222766 TTCGCGGCGCTTGAAAGTAA 61.223 50.000 30.54 7.86 0.00 2.24
6173 7671 1.017177 TCGCGGCGCTTGAAAGTAAT 61.017 50.000 30.54 0.00 0.00 1.89
6174 7672 0.179200 CGCGGCGCTTGAAAGTAATT 60.179 50.000 30.54 0.00 0.00 1.40
6175 7673 1.727857 CGCGGCGCTTGAAAGTAATTT 60.728 47.619 30.54 0.00 0.00 1.82
6176 7674 1.911464 GCGGCGCTTGAAAGTAATTTC 59.089 47.619 26.86 8.68 0.00 2.17
6177 7675 2.515912 CGGCGCTTGAAAGTAATTTCC 58.484 47.619 12.73 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.907197 ATTTATCTTCGAATGGCGTACTG 57.093 39.130 0.00 0.00 41.80 2.74
48 49 8.378565 TGAAGTAAGATCTGAGGAGTTCATTTT 58.621 33.333 0.00 0.00 34.68 1.82
69 70 5.009010 ACGCAATGATCAAGAAAGTTGAAGT 59.991 36.000 0.00 0.38 31.55 3.01
79 80 5.294306 GGAAGATACAACGCAATGATCAAGA 59.706 40.000 0.00 0.00 0.00 3.02
95 96 4.723309 AGCATGGATCAAAGGGAAGATAC 58.277 43.478 0.00 0.00 0.00 2.24
126 127 3.324268 TGTGATTGTAAACCGGTAGTGGA 59.676 43.478 8.00 0.00 0.00 4.02
210 211 0.322816 ATCGGCAGCATTGGAAGTGT 60.323 50.000 0.00 0.00 0.00 3.55
211 212 0.379669 GATCGGCAGCATTGGAAGTG 59.620 55.000 0.00 0.00 0.00 3.16
285 286 2.742053 GAGCTTCATCGCCAGTTTGTAA 59.258 45.455 0.00 0.00 0.00 2.41
287 288 1.160137 GAGCTTCATCGCCAGTTTGT 58.840 50.000 0.00 0.00 0.00 2.83
309 310 1.666189 GCTTGTCTAGGATGGAAACGC 59.334 52.381 0.00 0.00 0.00 4.84
368 369 1.274167 TGTCGGGTATGTGTGGAAGAC 59.726 52.381 0.00 0.00 0.00 3.01
385 386 4.340666 TCATCTGCTAGAAGACCTGATGTC 59.659 45.833 1.28 0.00 44.82 3.06
463 464 7.281324 CCACATGCCAATCATTCATTTGTTAAT 59.719 33.333 0.00 0.00 31.79 1.40
527 528 1.339631 CCCGTTGGGCAATCTAGACAA 60.340 52.381 0.00 0.00 35.35 3.18
560 561 3.581755 CCACATGCACTTTTGATCAAGG 58.418 45.455 8.41 8.39 0.00 3.61
589 590 9.915629 GATTGTTTGTACTCTATATGGAGTAGG 57.084 37.037 24.61 0.83 45.71 3.18
631 635 7.832187 TGGAAAACTCTCGGTATCCATAAATTT 59.168 33.333 0.00 0.00 38.39 1.82
632 636 7.343357 TGGAAAACTCTCGGTATCCATAAATT 58.657 34.615 0.00 0.00 38.39 1.82
633 637 6.895782 TGGAAAACTCTCGGTATCCATAAAT 58.104 36.000 0.00 0.00 38.39 1.40
634 638 6.302535 TGGAAAACTCTCGGTATCCATAAA 57.697 37.500 0.00 0.00 38.39 1.40
722 726 1.281199 TATGGGCTGTGCATGTCCCT 61.281 55.000 17.42 8.45 39.49 4.20
726 730 2.512692 TCTTTATGGGCTGTGCATGT 57.487 45.000 0.00 0.00 0.00 3.21
971 986 1.135731 GTCGCTGTGGTCTCTCTCG 59.864 63.158 0.00 0.00 0.00 4.04
1038 1053 0.244450 CCGTCACCTTGTAGCGGTTA 59.756 55.000 0.00 0.00 37.87 2.85
1226 1241 1.938069 AGGAAGCTAGGAAGGGGAGTA 59.062 52.381 0.00 0.00 0.00 2.59
1273 1290 5.416083 TGGAACCTCGTGTACAATTCATAG 58.584 41.667 0.00 0.00 0.00 2.23
1305 1336 3.403038 ACTGCAGACGAAGCAAATACTT 58.597 40.909 23.35 0.00 42.17 2.24
1456 1487 4.641094 AGTATCTGAAGAACTACCACGAGG 59.359 45.833 0.00 0.00 42.21 4.63
1539 1570 3.435327 GTCATGACCAACGAAGCATGTTA 59.565 43.478 15.31 0.00 39.22 2.41
1578 1609 2.516930 CATAAGGCTGGTGCGGGG 60.517 66.667 0.00 0.00 40.82 5.73
1582 1613 0.108138 ACGAGTCATAAGGCTGGTGC 60.108 55.000 0.00 0.00 38.76 5.01
1602 1633 3.760580 ACAAAAGGACAGAGAGAGGTG 57.239 47.619 0.00 0.00 0.00 4.00
1605 1636 7.793927 AACTAAAACAAAAGGACAGAGAGAG 57.206 36.000 0.00 0.00 0.00 3.20
1606 1637 9.273016 CATAACTAAAACAAAAGGACAGAGAGA 57.727 33.333 0.00 0.00 0.00 3.10
1720 1753 5.362430 ACAAAGGTAGTTTTGGCAAAGATGA 59.638 36.000 13.04 0.00 41.29 2.92
1765 1798 2.099141 TCGAAGCCATGAAAGGTCTG 57.901 50.000 0.00 0.00 0.00 3.51
1774 1807 7.387673 TCAGGTTAATAATGTATCGAAGCCATG 59.612 37.037 0.00 0.00 0.00 3.66
1777 1810 7.602644 TGATCAGGTTAATAATGTATCGAAGCC 59.397 37.037 0.00 0.00 0.00 4.35
1899 1932 2.697431 GCAACTTGCGGAATTGTGTA 57.303 45.000 0.00 0.00 31.71 2.90
1988 2021 7.703328 ACAAGTTACAACCTCAGTTAATGTTG 58.297 34.615 0.00 0.00 42.80 3.33
2096 2129 1.002857 CCTGGAGTTGGGGGAAATCT 58.997 55.000 0.00 0.00 0.00 2.40
2118 2151 3.834610 AGAATAAGAGTCCGTTGACACG 58.165 45.455 0.00 0.00 44.33 4.49
2127 2160 8.417884 ACTAGCAGATTACAAGAATAAGAGTCC 58.582 37.037 0.00 0.00 0.00 3.85
2149 2182 3.442076 AGTTGGTAAGGGTCCTGACTAG 58.558 50.000 4.61 0.00 0.00 2.57
2150 2183 3.555117 AGTTGGTAAGGGTCCTGACTA 57.445 47.619 4.61 0.00 0.00 2.59
2180 2213 6.800072 AAAGTTATTCAAAAACACCAGGGA 57.200 33.333 0.00 0.00 0.00 4.20
2313 2346 1.662629 CGAACATCATCACTGCCAGAC 59.337 52.381 0.00 0.00 0.00 3.51
2322 2355 1.276138 ACCTGCTCACGAACATCATCA 59.724 47.619 0.00 0.00 0.00 3.07
2397 2431 6.566079 AGTATCAGAATTGATGACTCCCAA 57.434 37.500 0.48 0.00 43.76 4.12
2398 2432 6.385176 AGAAGTATCAGAATTGATGACTCCCA 59.615 38.462 0.48 0.00 43.76 4.37
2399 2433 6.825610 AGAAGTATCAGAATTGATGACTCCC 58.174 40.000 0.48 0.00 43.76 4.30
2638 2672 9.716531 CTAATCACAGGAGAATATAGATGCAAA 57.283 33.333 0.00 0.00 0.00 3.68
2648 2682 8.589701 TGTTGACTACTAATCACAGGAGAATA 57.410 34.615 0.00 0.00 30.34 1.75
2890 2928 8.364142 AGAATCATATAGCAGAGAGTTGTAACC 58.636 37.037 0.00 0.00 0.00 2.85
3083 3121 5.988561 GGTGCAAAATGTAGTGAATCCAAAA 59.011 36.000 0.00 0.00 0.00 2.44
3224 3267 8.822652 AACAAAGATGAGTGATTCAAATTTCC 57.177 30.769 0.00 0.00 39.77 3.13
3292 4768 3.577415 ACTGTTGGGGTAAGAGTGTAGTC 59.423 47.826 0.00 0.00 40.97 2.59
3301 4777 3.485463 TCAGTCAACTGTTGGGGTAAG 57.515 47.619 19.55 5.58 44.12 2.34
3315 4791 3.196469 CAGACTAGGCAGGATTTCAGTCA 59.804 47.826 0.00 0.00 35.87 3.41
3356 4832 4.271687 GTTGTGTAAAACTTGACGAGCAG 58.728 43.478 0.00 0.00 0.00 4.24
3375 4851 2.620115 AGTGTGATCACAAAGCAGGTTG 59.380 45.455 29.42 0.00 46.01 3.77
3377 4853 2.645838 AGTGTGATCACAAAGCAGGT 57.354 45.000 29.42 6.32 46.01 4.00
3515 4995 9.163899 GATGATCAATGATGCACTGTAGAATAT 57.836 33.333 0.00 0.00 0.00 1.28
3662 5142 6.660521 AGAAACCATGTGAGAATATGCAGAAA 59.339 34.615 0.00 0.00 0.00 2.52
3698 5178 5.073965 ACAAACAAAGGTAATCCCCTAGACA 59.926 40.000 0.00 0.00 33.33 3.41
3699 5179 5.567430 ACAAACAAAGGTAATCCCCTAGAC 58.433 41.667 0.00 0.00 33.33 2.59
3878 5362 3.744426 TCTTAGGCGTGTTACTTTTGAGC 59.256 43.478 0.00 0.00 0.00 4.26
3948 5433 6.204688 TCAGCAACCAGTTTGTACAGAATAAG 59.795 38.462 0.00 0.00 37.54 1.73
4106 5591 8.038862 ACTTGATGACTAATACATGGATCCTT 57.961 34.615 14.23 3.29 0.00 3.36
4215 5700 3.737559 TGCACCAGAGGACCAATAATT 57.262 42.857 0.00 0.00 0.00 1.40
4224 5709 1.600638 CAGCAGATGCACCAGAGGA 59.399 57.895 7.68 0.00 45.16 3.71
4339 5824 9.577110 AATTTGCATGTAATCTGAATAACAGTG 57.423 29.630 0.00 0.00 45.86 3.66
4365 5850 6.983890 GGGAAAACTCAAAATAGAAGTGCAAA 59.016 34.615 0.00 0.00 0.00 3.68
4567 6052 4.212636 TCAATCATCTGCGCATAGACATTG 59.787 41.667 12.24 16.53 34.55 2.82
4672 6157 1.008327 TCCTCCATCCAGTAAGCCTCA 59.992 52.381 0.00 0.00 0.00 3.86
4778 6263 0.179073 CCGACCTGTATTCAGCCCAG 60.179 60.000 0.00 0.00 40.09 4.45
4901 6386 5.990996 TGGTCAAATCTGCAAAAGGAATTTC 59.009 36.000 0.00 0.00 0.00 2.17
4976 6463 0.326927 AACCATGACCTTACCCCACG 59.673 55.000 0.00 0.00 0.00 4.94
5302 6792 7.866393 AGCAACGACACAGGTATACTAATAATC 59.134 37.037 2.25 0.00 0.00 1.75
5339 6829 7.827819 ACATGCAAATCAAAATTGATCAGAG 57.172 32.000 8.96 4.01 46.60 3.35
5341 6831 7.118535 TGGAACATGCAAATCAAAATTGATCAG 59.881 33.333 8.96 6.33 46.60 2.90
5370 6860 4.586421 TGTAATCACAATGCCCTTGTCAAA 59.414 37.500 0.00 0.00 44.99 2.69
5499 6989 7.395190 TTGCTTGCTCATTTGTGATATAAGT 57.605 32.000 0.00 0.00 0.00 2.24
5500 6990 8.752254 CAATTGCTTGCTCATTTGTGATATAAG 58.248 33.333 0.00 0.00 0.00 1.73
5501 6991 8.252417 ACAATTGCTTGCTCATTTGTGATATAA 58.748 29.630 5.05 0.00 38.40 0.98
5502 6992 7.774134 ACAATTGCTTGCTCATTTGTGATATA 58.226 30.769 5.05 0.00 38.40 0.86
5503 6993 6.636705 ACAATTGCTTGCTCATTTGTGATAT 58.363 32.000 5.05 0.00 38.40 1.63
5504 6994 6.028146 ACAATTGCTTGCTCATTTGTGATA 57.972 33.333 5.05 0.00 38.40 2.15
5505 6995 4.890088 ACAATTGCTTGCTCATTTGTGAT 58.110 34.783 5.05 0.00 38.40 3.06
5506 6996 4.325028 ACAATTGCTTGCTCATTTGTGA 57.675 36.364 5.05 0.00 38.40 3.58
5507 6997 4.375606 CGAACAATTGCTTGCTCATTTGTG 60.376 41.667 5.05 0.00 39.22 3.33
5508 6998 3.737266 CGAACAATTGCTTGCTCATTTGT 59.263 39.130 5.05 7.89 40.27 2.83
5514 7004 4.360482 GTTTTCGAACAATTGCTTGCTC 57.640 40.909 5.05 0.00 35.69 4.26
5557 7047 1.000163 GGTCGAACAAGAGCAGAGACA 60.000 52.381 0.00 0.00 38.41 3.41
5566 7056 2.159430 CGCAATGAATGGTCGAACAAGA 59.841 45.455 7.51 0.00 0.00 3.02
5570 7060 1.463056 TGACGCAATGAATGGTCGAAC 59.537 47.619 0.00 0.00 34.09 3.95
5586 7076 1.638133 CAGAGACAATGAGCCTGACG 58.362 55.000 0.00 0.00 0.00 4.35
5598 7088 4.040339 TGAATGGTAAGAAGTGCAGAGACA 59.960 41.667 0.00 0.00 0.00 3.41
5625 7117 4.082949 ACACCGATGTTTAAAAGCCTAAGC 60.083 41.667 0.00 0.00 34.46 3.09
5626 7118 5.622770 ACACCGATGTTTAAAAGCCTAAG 57.377 39.130 0.00 0.00 34.46 2.18
5628 7120 5.797051 AGTACACCGATGTTTAAAAGCCTA 58.203 37.500 0.00 0.00 40.48 3.93
5634 7126 5.613329 ACAAGGAGTACACCGATGTTTAAA 58.387 37.500 14.75 0.00 40.48 1.52
5635 7127 5.217978 ACAAGGAGTACACCGATGTTTAA 57.782 39.130 14.75 0.00 40.48 1.52
5636 7128 4.322198 GGACAAGGAGTACACCGATGTTTA 60.322 45.833 19.21 0.00 40.48 2.01
5804 7302 4.849310 CGGTGCACCATACCCCGG 62.849 72.222 34.16 12.56 34.66 5.73
5806 7304 4.109675 AGCGGTGCACCATACCCC 62.110 66.667 34.16 14.73 34.66 4.95
5807 7305 2.824041 CAGCGGTGCACCATACCC 60.824 66.667 34.16 16.43 34.66 3.69
5808 7306 2.824041 CCAGCGGTGCACCATACC 60.824 66.667 34.16 18.83 35.14 2.73
5809 7307 2.824041 CCCAGCGGTGCACCATAC 60.824 66.667 34.16 22.51 35.14 2.39
5810 7308 4.108299 CCCCAGCGGTGCACCATA 62.108 66.667 34.16 0.00 35.14 2.74
5899 7397 2.557805 GTCGTCTACGTGACCGCA 59.442 61.111 0.00 0.00 42.49 5.69
5923 7421 1.868251 GCTCATCACCGTCGTCGTC 60.868 63.158 0.71 0.00 35.01 4.20
6031 7529 0.113580 TCATGATCGGGATCGGGGTA 59.886 55.000 4.36 0.00 40.63 3.69
6094 7592 8.552034 GTGTGGATTAATAATAAGAGCACACTC 58.448 37.037 0.11 0.00 43.82 3.51
6100 7598 6.770785 TGGTGGTGTGGATTAATAATAAGAGC 59.229 38.462 0.00 0.00 0.00 4.09
6101 7599 8.924511 ATGGTGGTGTGGATTAATAATAAGAG 57.075 34.615 0.00 0.00 0.00 2.85
6102 7600 9.349713 GAATGGTGGTGTGGATTAATAATAAGA 57.650 33.333 0.00 0.00 0.00 2.10
6103 7601 9.354673 AGAATGGTGGTGTGGATTAATAATAAG 57.645 33.333 0.00 0.00 0.00 1.73
6111 7609 4.927267 AGAAGAATGGTGGTGTGGATTA 57.073 40.909 0.00 0.00 0.00 1.75
6123 7621 2.304751 GCATTGGGCAAGAAGAATGG 57.695 50.000 0.00 0.00 43.97 3.16
6147 7645 4.101790 AAGCGCCGCGAAACCATG 62.102 61.111 18.91 0.00 0.00 3.66
6148 7646 4.101790 CAAGCGCCGCGAAACCAT 62.102 61.111 18.91 0.00 0.00 3.55
6150 7648 3.530398 TTTCAAGCGCCGCGAAACC 62.530 57.895 18.91 0.00 0.00 3.27
6151 7649 2.051703 TTTCAAGCGCCGCGAAAC 60.052 55.556 18.91 0.00 0.00 2.78
6152 7650 1.222766 TACTTTCAAGCGCCGCGAAA 61.223 50.000 18.91 10.01 0.00 3.46
6153 7651 1.222766 TTACTTTCAAGCGCCGCGAA 61.223 50.000 18.91 0.91 0.00 4.70
6154 7652 1.017177 ATTACTTTCAAGCGCCGCGA 61.017 50.000 18.91 0.00 0.00 5.87
6155 7653 0.179200 AATTACTTTCAAGCGCCGCG 60.179 50.000 8.83 8.83 0.00 6.46
6156 7654 1.911464 GAAATTACTTTCAAGCGCCGC 59.089 47.619 2.29 0.00 40.45 6.53
6157 7655 2.515912 GGAAATTACTTTCAAGCGCCG 58.484 47.619 2.29 0.00 42.17 6.46


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

AutoCloner maintained by Alex Coulton.