Multiple sequence alignment - TraesCS2A01G347900

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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 TraesCS2A01G347900 chr2A 100.000 8512 0 0 1 8512 586449276 586457787 0.000000e+00 15719
1 TraesCS2A01G347900 chr2B 92.740 7741 276 102 1 7602 522082531 522090124 0.000000e+00 10918
2 TraesCS2A01G347900 chr2B 94.686 414 20 2 8100 8512 522090897 522091309 7.200000e-180 641
3 TraesCS2A01G347900 chr2B 91.803 305 24 1 7567 7871 522090125 522090428 2.840000e-114 424
4 TraesCS2A01G347900 chr2B 96.575 146 3 1 7955 8098 522090628 522090773 3.070000e-59 241
5 TraesCS2A01G347900 chr2B 93.431 137 7 2 5526 5661 166470771 166470906 1.450000e-47 202
6 TraesCS2A01G347900 chr2D 92.982 7566 294 72 795 8230 442982363 442989821 0.000000e+00 10811
7 TraesCS2A01G347900 chr2D 95.934 787 10 7 1 787 442979931 442980695 0.000000e+00 1256
8 TraesCS2A01G347900 chr2D 95.918 294 11 1 8219 8512 442989844 442990136 7.730000e-130 475
9 TraesCS2A01G347900 chr2D 92.647 136 7 3 5526 5660 388833791 388833658 8.720000e-45 193
10 TraesCS2A01G347900 chr6D 92.754 138 8 2 5526 5661 210769653 210769516 1.870000e-46 198
11 TraesCS2A01G347900 chr6D 94.574 129 6 1 5526 5653 365847011 365846883 1.870000e-46 198
12 TraesCS2A01G347900 chr6A 93.233 133 8 1 5521 5652 506642961 506642829 2.420000e-45 195
13 TraesCS2A01G347900 chr3B 92.701 137 6 3 5526 5661 254939043 254939176 2.420000e-45 195
14 TraesCS2A01G347900 chr3B 91.892 74 6 0 4599 4672 447635506 447635579 4.200000e-18 104
15 TraesCS2A01G347900 chr3A 92.593 135 8 2 5526 5659 464907578 464907711 8.720000e-45 193
16 TraesCS2A01G347900 chr3A 75.704 284 39 15 4599 4874 466803537 466803798 1.940000e-21 115
17 TraesCS2A01G347900 chr3D 82.707 133 18 5 4559 4690 105171181 105171309 6.980000e-21 113
18 TraesCS2A01G347900 chr3D 82.707 133 18 5 4559 4690 105194382 105194510 6.980000e-21 113
19 TraesCS2A01G347900 chr3D 82.707 133 18 5 4559 4690 105248958 105249086 6.980000e-21 113
20 TraesCS2A01G347900 chr3D 82.707 133 18 5 4559 4690 105276569 105276697 6.980000e-21 113
21 TraesCS2A01G347900 chr3D 91.892 74 6 0 4599 4672 347598702 347598775 4.200000e-18 104


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 TraesCS2A01G347900 chr2A 586449276 586457787 8511 False 15719.000000 15719 100.000000 1 8512 1 chr2A.!!$F1 8511
1 TraesCS2A01G347900 chr2B 522082531 522091309 8778 False 3056.000000 10918 93.951000 1 8512 4 chr2B.!!$F2 8511
2 TraesCS2A01G347900 chr2D 442979931 442990136 10205 False 4180.666667 10811 94.944667 1 8512 3 chr2D.!!$F1 8511

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
431 435 0.041833 CAGGAACAGGAGGAGGAGGA 59.958 60.000 0.00 0.00 0.00 3.71 F
917 2601 0.258774 GTCTACCCACCCCGTACCTA 59.741 60.000 0.00 0.00 0.00 3.08 F
921 2605 0.259938 ACCCACCCCGTACCTACTAG 59.740 60.000 0.00 0.00 0.00 2.57 F
1390 3101 0.987294 AGCCAACACTATGGTGAGCT 59.013 50.000 16.98 16.44 45.61 4.09 F
1461 3173 1.667830 CACGGATTGTGGCGAGTGT 60.668 57.895 0.00 0.00 45.21 3.55 F
2526 4264 0.450983 GCCTCATCTGCTTGCAGTTC 59.549 55.000 20.20 0.00 0.00 3.01 F
3791 5585 0.178301 TGGGACACACTACGTTTGCA 59.822 50.000 0.00 0.00 0.00 4.08 F
4191 5988 0.602562 TGCATTTACTTGGCCACTGC 59.397 50.000 3.88 8.75 0.00 4.40 F
5708 7517 0.314935 TCCCGTACCTTGTCACGAAC 59.685 55.000 0.00 0.00 40.56 3.95 F
6884 8702 1.667724 CTGCAGGCCTATCTTGAAACG 59.332 52.381 3.98 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 3136 0.385751 GGCATACAGAGACAGCGCTA 59.614 55.000 10.99 0.00 0.00 4.26 R
2177 3909 0.392998 CAGGTCATGGTAGTGGGCAC 60.393 60.000 0.00 0.00 0.00 5.01 R
2178 3910 0.546507 TCAGGTCATGGTAGTGGGCA 60.547 55.000 0.00 0.00 0.00 5.36 R
2473 4208 0.681564 AGTACCAGACAGCCTCTCGG 60.682 60.000 0.00 0.00 0.00 4.63 R
2877 4615 1.822990 AGCAAGCATCACATGGAAAGG 59.177 47.619 0.00 0.00 0.00 3.11 R
3914 5709 1.608590 AGTTTTGACAAGATGGCACCG 59.391 47.619 0.00 0.00 33.32 4.94 R
4777 6575 1.202927 ACTACAACACCTGCATGGCTT 60.203 47.619 0.00 0.00 40.22 4.35 R
6177 7989 1.890489 TCGCAGGCTCTAACAACACTA 59.110 47.619 0.00 0.00 0.00 2.74 R
6922 8740 0.690744 ACAAAAGTTGGCTGCCCCTT 60.691 50.000 17.53 14.99 34.12 3.95 R
8425 10567 0.598065 AACCTCGGCTTTCATTGCAC 59.402 50.000 0.00 0.00 0.00 4.57 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
431 435 0.041833 CAGGAACAGGAGGAGGAGGA 59.958 60.000 0.00 0.00 0.00 3.71
432 436 0.338120 AGGAACAGGAGGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
433 437 1.334384 GGAACAGGAGGAGGAGGAGC 61.334 65.000 0.00 0.00 0.00 4.70
462 466 1.378250 GCAGCAACAGCAGGAGGAT 60.378 57.895 0.00 0.00 0.00 3.24
595 605 1.006102 AAGAAGTGGACGACGCCAG 60.006 57.895 10.64 0.00 38.95 4.85
596 606 2.432628 GAAGTGGACGACGCCAGG 60.433 66.667 10.64 0.00 38.95 4.45
597 607 4.681978 AAGTGGACGACGCCAGGC 62.682 66.667 0.00 0.00 38.95 4.85
655 665 4.267349 AGAATGTGTGGTGGTACTGTAC 57.733 45.455 9.46 9.46 0.00 2.90
788 806 6.880529 TCTCCCGTCCGAGTAAAATAATTTTT 59.119 34.615 0.00 0.00 38.56 1.94
793 811 9.906111 CCGTCCGAGTAAAATAATTTTTAGTAC 57.094 33.333 2.47 0.00 39.79 2.73
911 2595 2.284405 ACTGGTCTACCCACCCCG 60.284 66.667 0.00 0.00 38.72 5.73
912 2596 2.284405 CTGGTCTACCCACCCCGT 60.284 66.667 0.00 0.00 38.72 5.28
913 2597 1.000739 CTGGTCTACCCACCCCGTA 59.999 63.158 0.00 0.00 38.72 4.02
914 2598 1.305213 TGGTCTACCCACCCCGTAC 60.305 63.158 0.00 0.00 38.72 3.67
915 2599 2.060383 GGTCTACCCACCCCGTACC 61.060 68.421 0.00 0.00 0.00 3.34
916 2600 1.000866 GTCTACCCACCCCGTACCT 59.999 63.158 0.00 0.00 0.00 3.08
917 2601 0.258774 GTCTACCCACCCCGTACCTA 59.741 60.000 0.00 0.00 0.00 3.08
921 2605 0.259938 ACCCACCCCGTACCTACTAG 59.740 60.000 0.00 0.00 0.00 2.57
960 2644 1.957186 CGACAGCGACGGGGAAAAA 60.957 57.895 0.00 0.00 40.82 1.94
1237 2948 1.142060 AGGTGTTTGACGGAATGGTGA 59.858 47.619 0.00 0.00 0.00 4.02
1238 2949 1.265905 GGTGTTTGACGGAATGGTGAC 59.734 52.381 0.00 0.00 0.00 3.67
1380 3091 1.371558 GGACGAAGGAGCCAACACT 59.628 57.895 0.00 0.00 0.00 3.55
1390 3101 0.987294 AGCCAACACTATGGTGAGCT 59.013 50.000 16.98 16.44 45.61 4.09
1404 3115 3.316029 TGGTGAGCTCATTTCTGTTTGTG 59.684 43.478 21.47 0.00 0.00 3.33
1424 3136 2.946329 TGAATAACTTGTGGCGTTGTGT 59.054 40.909 0.00 0.00 0.00 3.72
1426 3138 4.212425 TGAATAACTTGTGGCGTTGTGTAG 59.788 41.667 0.00 0.00 0.00 2.74
1461 3173 1.667830 CACGGATTGTGGCGAGTGT 60.668 57.895 0.00 0.00 45.21 3.55
1499 3211 5.220529 GCGACCTGTGTACATTATGGTTTAC 60.221 44.000 0.00 0.00 0.00 2.01
1630 3361 7.816995 CCTAGAAGATTAGCTGATGACATAACC 59.183 40.741 0.00 0.00 0.00 2.85
1635 3366 7.385267 AGATTAGCTGATGACATAACCTGATC 58.615 38.462 0.00 0.00 0.00 2.92
1640 3371 5.282055 TGATGACATAACCTGATCCTGTC 57.718 43.478 0.00 0.00 37.36 3.51
1644 3375 2.505819 ACATAACCTGATCCTGTCACCC 59.494 50.000 0.00 0.00 32.22 4.61
1803 3535 7.639113 TGTTCCCATCAATGAATTACCTTAC 57.361 36.000 0.00 0.00 0.00 2.34
1982 3714 5.339035 CCATAAGATCCCTTCAGATCCCATC 60.339 48.000 0.00 0.00 43.14 3.51
2174 3906 9.162764 ACATTTTATCGATTGCTAGTGTTAGTT 57.837 29.630 1.71 0.00 0.00 2.24
2175 3907 9.988350 CATTTTATCGATTGCTAGTGTTAGTTT 57.012 29.630 1.71 0.00 0.00 2.66
2178 3910 9.865321 TTTATCGATTGCTAGTGTTAGTTTAGT 57.135 29.630 1.71 0.00 0.00 2.24
2243 3978 7.636150 ATTGACAATTTGTAGATTCTCCAGG 57.364 36.000 1.15 0.00 0.00 4.45
2250 3985 7.929941 ATTTGTAGATTCTCCAGGTCTTTTC 57.070 36.000 0.00 0.00 0.00 2.29
2512 4250 4.417437 ACTCTAGTGTTCCTTAAGCCTCA 58.583 43.478 0.00 0.00 0.00 3.86
2513 4251 5.026790 ACTCTAGTGTTCCTTAAGCCTCAT 58.973 41.667 0.00 0.00 0.00 2.90
2514 4252 5.128008 ACTCTAGTGTTCCTTAAGCCTCATC 59.872 44.000 0.00 0.00 0.00 2.92
2526 4264 0.450983 GCCTCATCTGCTTGCAGTTC 59.549 55.000 20.20 0.00 0.00 3.01
2682 4420 4.522722 AGAGGTGAGTTCTTTCCTTACG 57.477 45.455 0.00 0.00 0.00 3.18
2691 4429 5.665459 AGTTCTTTCCTTACGGATCATCAG 58.335 41.667 0.00 0.00 39.58 2.90
2877 4615 3.913548 TGTGCACAAACACCATATGAC 57.086 42.857 19.28 0.00 39.93 3.06
2979 4719 6.164417 TGTACTGGCTTTGAGTAACAACTA 57.836 37.500 0.00 0.00 38.29 2.24
3441 5233 2.507407 TGGAGTTGGACTAATTGGCC 57.493 50.000 0.00 0.00 46.75 5.36
3457 5249 1.180029 GGCCATGCAACAGAACTGAT 58.820 50.000 8.87 0.00 0.00 2.90
3459 5251 2.754552 GGCCATGCAACAGAACTGATTA 59.245 45.455 8.87 0.00 0.00 1.75
3583 5377 6.153340 CCCAATAATATGCATCTTCCCGAAAT 59.847 38.462 0.19 0.00 0.00 2.17
3588 5382 6.992063 ATATGCATCTTCCCGAAATCATAC 57.008 37.500 0.19 0.00 0.00 2.39
3791 5585 0.178301 TGGGACACACTACGTTTGCA 59.822 50.000 0.00 0.00 0.00 4.08
3809 5603 6.242829 GTTTGCAGTTTCAACTTGTCATTTG 58.757 36.000 0.00 0.00 37.08 2.32
3840 5634 4.979197 GCATGTTGTTGTCGTAAATTTGGA 59.021 37.500 0.00 0.00 0.00 3.53
3876 5671 4.331968 TGTTCCCAGTTATGGTGATTCAC 58.668 43.478 8.34 8.34 46.10 3.18
3914 5709 3.632604 TCAGGTATGGTTCTCTCATCGTC 59.367 47.826 0.00 0.00 0.00 4.20
3969 5764 2.363306 TTCAGCAAAGAAAGGAGGCA 57.637 45.000 0.00 0.00 0.00 4.75
4070 5867 7.717436 TGTCATGTCATTTCCTTTGTTAGTGTA 59.283 33.333 0.00 0.00 0.00 2.90
4107 5904 1.985662 CCCGCGTATGGGCCCTATA 60.986 63.158 25.70 16.01 43.70 1.31
4185 5982 3.057315 TGAAAGAGCTGCATTTACTTGGC 60.057 43.478 1.02 0.00 0.00 4.52
4191 5988 0.602562 TGCATTTACTTGGCCACTGC 59.397 50.000 3.88 8.75 0.00 4.40
4234 6032 4.439700 CCATTCAAGGATGCATGTTCACTC 60.440 45.833 2.46 0.00 29.40 3.51
4258 6056 6.992123 TCGATGAACCAGCATCACTATTTTAT 59.008 34.615 0.00 0.00 43.76 1.40
4335 6133 4.227073 TCCATTTACACCCTGTCATGATCA 59.773 41.667 0.00 0.00 0.00 2.92
4357 6155 5.871524 TCACTGCTGATTTCTGTATTGACTC 59.128 40.000 0.00 0.00 0.00 3.36
4466 6264 3.602915 GCTACGTAGTTGTCGAGAAACAG 59.397 47.826 22.98 6.60 37.78 3.16
4495 6293 6.716628 TGCAAGATGAGAAATAAGTCAAAGGT 59.283 34.615 0.00 0.00 0.00 3.50
4501 6299 9.771534 GATGAGAAATAAGTCAAAGGTAGCTAT 57.228 33.333 0.00 0.00 0.00 2.97
4509 6307 9.988815 ATAAGTCAAAGGTAGCTATGATACAAG 57.011 33.333 0.00 0.00 0.00 3.16
4570 6368 4.218200 CACAACATTCATGGCCAGTTTAGA 59.782 41.667 13.05 0.65 0.00 2.10
4572 6370 4.307032 ACATTCATGGCCAGTTTAGACT 57.693 40.909 13.05 0.00 36.25 3.24
4614 6412 2.093341 GGGGGTGTTGACGTATATGTGT 60.093 50.000 1.31 0.00 0.00 3.72
4643 6441 4.338879 CAACCTTCTCCATCAGTTTGGAT 58.661 43.478 0.00 0.00 44.66 3.41
4672 6470 5.411669 GGTTCTTCTCGTTGGTACATGAAAT 59.588 40.000 0.00 0.00 39.30 2.17
4775 6573 2.028748 TCTGTCCACGTTTAGGCCTTAC 60.029 50.000 12.58 9.30 0.00 2.34
4777 6575 1.002315 GTCCACGTTTAGGCCTTACCA 59.998 52.381 12.58 0.00 43.14 3.25
4786 6584 4.016838 GCCTTACCAAGCCATGCA 57.983 55.556 0.00 0.00 0.00 3.96
4876 6682 9.301153 CTGGTTGGTGCATAAAACTTAATATTC 57.699 33.333 0.00 0.00 0.00 1.75
5232 7038 4.060900 CTCACGCATGACTGGCTATTATT 58.939 43.478 0.00 0.00 0.00 1.40
5239 7045 8.528643 ACGCATGACTGGCTATTATTACTATTA 58.471 33.333 0.00 0.00 0.00 0.98
5320 7126 2.912295 TGTCCAATGTCCAGAGGATGAA 59.088 45.455 0.00 0.00 32.73 2.57
5465 7274 5.105595 GGGAAATTTGTCTCAATCCCTTCAG 60.106 44.000 0.00 0.00 42.64 3.02
5471 7280 3.006247 GTCTCAATCCCTTCAGCAGTTC 58.994 50.000 0.00 0.00 0.00 3.01
5479 7288 3.573967 TCCCTTCAGCAGTTCCATTTTTC 59.426 43.478 0.00 0.00 0.00 2.29
5513 7322 2.814805 ACAAGAGCCATATTGCTGGT 57.185 45.000 5.94 0.00 42.95 4.00
5516 7325 3.194116 ACAAGAGCCATATTGCTGGTTTG 59.806 43.478 5.94 10.02 42.95 2.93
5609 7418 8.361139 CGATATCTTATGGGTTTCAACTCTAGT 58.639 37.037 0.34 0.00 0.00 2.57
5641 7450 2.693074 TGTTTGGGACTGAAAGGCTTTC 59.307 45.455 28.71 28.71 46.21 2.62
5676 7485 4.983538 TGTTGTTGCTTCTACATTTGCATG 59.016 37.500 0.00 0.00 35.27 4.06
5708 7517 0.314935 TCCCGTACCTTGTCACGAAC 59.685 55.000 0.00 0.00 40.56 3.95
5761 7570 2.184533 TGGTCTATTTCAGAAGGCGGA 58.815 47.619 0.00 0.00 34.17 5.54
6029 7841 5.103982 TCCATCATCAAAGGATTCCTTGCTA 60.104 40.000 18.63 7.76 43.92 3.49
6031 7843 4.191544 TCATCAAAGGATTCCTTGCTACG 58.808 43.478 18.63 7.16 43.92 3.51
6090 7902 8.506168 GGAATCACATTTCCACTGTTAAGATA 57.494 34.615 0.00 0.00 43.92 1.98
6114 7926 4.472496 TCTGTTGTACCAGTACCACTGTA 58.528 43.478 11.94 2.40 44.50 2.74
6160 7972 7.012661 TGATACATATGCACTTGGAGATCAT 57.987 36.000 1.58 0.00 0.00 2.45
6177 7989 6.222038 AGATCATATCACAACACCGTACTT 57.778 37.500 0.00 0.00 0.00 2.24
6194 8006 4.857588 CGTACTTAGTGTTGTTAGAGCCTG 59.142 45.833 0.00 0.00 0.00 4.85
6217 8029 6.541969 TGCGAGTTATTGTATCACAACATTG 58.458 36.000 0.00 0.00 41.40 2.82
6249 8061 6.070021 TGACCTATGAGATGTGGACTGATTTT 60.070 38.462 0.00 0.00 0.00 1.82
6349 8161 7.710044 ACATGTGTAGCAGAATCTCATCTTAAG 59.290 37.037 0.00 0.00 0.00 1.85
6521 8337 6.998673 AGGTTCAGCTTTATACTTGAACTGTT 59.001 34.615 13.77 0.00 45.32 3.16
6602 8418 4.919168 CCAGTTTTCGTGTACTCGTGATTA 59.081 41.667 16.12 0.00 0.00 1.75
6884 8702 1.667724 CTGCAGGCCTATCTTGAAACG 59.332 52.381 3.98 0.00 0.00 3.60
6922 8740 3.264964 CCTTACAAAGCTACTGGGGGTAA 59.735 47.826 0.00 0.00 0.00 2.85
7004 8822 2.353605 CCTGTGCTTGTGTTGTGGTTTT 60.354 45.455 0.00 0.00 0.00 2.43
7218 9036 2.171003 GGCAAGTCAATAAAGCCACCT 58.829 47.619 0.00 0.00 44.59 4.00
7292 9110 7.543520 GGAAATGAAGCTCTAACAAAAGAATGG 59.456 37.037 0.00 0.00 0.00 3.16
7310 9135 7.913674 AGAATGGACATCTAAAAACAGTCTC 57.086 36.000 0.00 0.00 28.56 3.36
7313 9138 5.607477 TGGACATCTAAAAACAGTCTCGTT 58.393 37.500 0.00 0.00 0.00 3.85
7353 9178 4.881850 AGCAAACCAGAAATAGTAATCCCG 59.118 41.667 0.00 0.00 0.00 5.14
7363 9191 1.276622 AGTAATCCCGCCAAGTGACT 58.723 50.000 0.00 0.00 0.00 3.41
7519 9348 7.445900 TCAAGCAAGTTAGTTAATATCGACG 57.554 36.000 0.00 0.00 0.00 5.12
7641 9506 2.332063 AACCAGGCATCCAGTATTCG 57.668 50.000 0.00 0.00 0.00 3.34
7703 9568 0.994995 CTGATCGCCTGAAGTGTTCG 59.005 55.000 0.00 0.00 0.00 3.95
7709 9574 1.870580 CGCCTGAAGTGTTCGTGGTTA 60.871 52.381 0.00 0.00 0.00 2.85
7723 9588 7.858879 GTGTTCGTGGTTATTTTGAACAGTAAT 59.141 33.333 6.36 0.00 46.59 1.89
7833 9698 2.267006 CTGCATGGTGCTCGAGGT 59.733 61.111 15.58 0.00 45.31 3.85
7834 9699 2.046988 TGCATGGTGCTCGAGGTG 60.047 61.111 15.58 0.00 45.31 4.00
7842 9707 1.531578 GGTGCTCGAGGTGTTTCTTTC 59.468 52.381 15.58 0.00 0.00 2.62
7846 9711 1.801178 CTCGAGGTGTTTCTTTCTGCC 59.199 52.381 3.91 0.00 0.00 4.85
7883 9780 1.668419 ACAGTGTGGCTCTGAACAAC 58.332 50.000 0.00 0.00 36.81 3.32
7903 9800 0.806868 AATGATCTGTGCGTTGCAGG 59.193 50.000 0.00 0.00 40.08 4.85
8045 10030 5.939883 TGTCTTGTTCAACTATCTTGGGATG 59.060 40.000 0.00 0.00 33.71 3.51
8234 10375 1.246056 ATGCGTGCTCCACTTGCAAT 61.246 50.000 0.00 0.00 42.41 3.56
8254 10395 6.742109 GCAATGTGCATAATTATGTTCCTCT 58.258 36.000 23.14 5.18 44.26 3.69
8259 10400 8.213518 TGTGCATAATTATGTTCCTCTCTTTC 57.786 34.615 23.14 5.99 36.11 2.62
8425 10567 2.159599 GGTACGTTCACCTCTGTAGACG 60.160 54.545 0.00 0.00 37.72 4.18
8433 10575 1.893137 ACCTCTGTAGACGTGCAATGA 59.107 47.619 0.00 0.00 0.00 2.57
8437 10579 2.736721 TCTGTAGACGTGCAATGAAAGC 59.263 45.455 0.00 0.00 0.00 3.51
8452 10594 2.629137 TGAAAGCCGAGGTTGTGTAGTA 59.371 45.455 0.00 0.00 0.00 1.82
8490 10632 5.957771 ATCAAGGAGGCATTACAGTAGAA 57.042 39.130 0.00 0.00 0.00 2.10
8492 10634 4.162320 TCAAGGAGGCATTACAGTAGAAGG 59.838 45.833 0.00 0.00 0.00 3.46
8494 10636 4.880164 AGGAGGCATTACAGTAGAAGGTA 58.120 43.478 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
560 570 1.211212 TCTTGATGAGGCAGGTGATGG 59.789 52.381 0.00 0.00 0.00 3.51
655 665 3.976169 ACATTTTTGGTGAATGTGACGG 58.024 40.909 2.02 0.00 43.87 4.79
788 806 0.608856 TGTTCCGGGAGCACGTACTA 60.609 55.000 9.73 0.00 0.00 1.82
848 2532 0.806102 CCTGGTTATGCCACGACGAG 60.806 60.000 0.00 0.00 43.61 4.18
849 2533 1.216977 CCTGGTTATGCCACGACGA 59.783 57.895 0.00 0.00 43.61 4.20
911 2595 2.139118 CCGCGGAGTACTAGTAGGTAC 58.861 57.143 24.07 0.00 41.47 3.34
912 2596 1.541233 GCCGCGGAGTACTAGTAGGTA 60.541 57.143 33.48 0.00 0.00 3.08
913 2597 0.817229 GCCGCGGAGTACTAGTAGGT 60.817 60.000 33.48 0.00 0.00 3.08
914 2598 0.534652 AGCCGCGGAGTACTAGTAGG 60.535 60.000 33.48 0.95 0.00 3.18
915 2599 0.867086 GAGCCGCGGAGTACTAGTAG 59.133 60.000 33.48 0.00 0.00 2.57
916 2600 0.533755 GGAGCCGCGGAGTACTAGTA 60.534 60.000 33.48 0.00 0.00 1.82
917 2601 1.823041 GGAGCCGCGGAGTACTAGT 60.823 63.158 33.48 0.00 0.00 2.57
921 2605 3.539560 GATCGGAGCCGCGGAGTAC 62.540 68.421 33.48 15.48 39.59 2.73
954 2638 2.172659 GCCGCTCGTCGTTTTTCC 59.827 61.111 0.00 0.00 36.19 3.13
1020 2704 2.445654 GAGCAGGAGGAGGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
1380 3091 5.181811 CACAAACAGAAATGAGCTCACCATA 59.818 40.000 20.97 0.00 0.00 2.74
1390 3101 7.920151 CCACAAGTTATTCACAAACAGAAATGA 59.080 33.333 0.00 0.00 0.00 2.57
1404 3115 3.619233 ACACAACGCCACAAGTTATTC 57.381 42.857 0.00 0.00 0.00 1.75
1424 3136 0.385751 GGCATACAGAGACAGCGCTA 59.614 55.000 10.99 0.00 0.00 4.26
1426 3138 1.153568 TGGCATACAGAGACAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
1458 3170 1.210155 GCACCATTCGCTCCAACAC 59.790 57.895 0.00 0.00 0.00 3.32
1461 3173 2.032634 GTCGCACCATTCGCTCCAA 61.033 57.895 0.00 0.00 0.00 3.53
1499 3211 0.455633 GCAATTGCGACAAGGAGCAG 60.456 55.000 15.87 0.00 44.72 4.24
1525 3237 8.450964 ACACACAAACACATGCTTCTTATATAC 58.549 33.333 0.00 0.00 0.00 1.47
1630 3361 1.153489 CTGCGGGTGACAGGATCAG 60.153 63.158 0.00 0.00 38.28 2.90
1640 3371 1.845809 GCACTTTCTGTCTGCGGGTG 61.846 60.000 0.00 0.00 0.00 4.61
1644 3375 1.400629 CCAATGCACTTTCTGTCTGCG 60.401 52.381 0.00 0.00 0.00 5.18
1762 3494 5.049060 TGGGAACAATTTACAGACGACAATG 60.049 40.000 0.00 0.00 37.44 2.82
1803 3535 6.506500 AGGCTGAAATAGACATTGAACTTG 57.493 37.500 0.00 0.00 36.64 3.16
1817 3549 1.635487 TGCTGGGAGTTAGGCTGAAAT 59.365 47.619 0.00 0.00 0.00 2.17
2043 3775 5.640189 TGTACTGTAGGCTGAAGTAGTTC 57.360 43.478 10.38 3.15 0.00 3.01
2174 3906 1.557832 GGTCATGGTAGTGGGCACTAA 59.442 52.381 0.00 0.00 44.62 2.24
2175 3907 1.200519 GGTCATGGTAGTGGGCACTA 58.799 55.000 0.00 0.00 42.54 2.74
2176 3908 0.547712 AGGTCATGGTAGTGGGCACT 60.548 55.000 0.00 0.00 45.02 4.40
2177 3909 0.392998 CAGGTCATGGTAGTGGGCAC 60.393 60.000 0.00 0.00 0.00 5.01
2178 3910 0.546507 TCAGGTCATGGTAGTGGGCA 60.547 55.000 0.00 0.00 0.00 5.36
2243 3978 8.278408 GCAGAATCAAATTTGAAAGGAAAAGAC 58.722 33.333 23.91 7.00 41.13 3.01
2250 3985 6.684686 TCAGAGCAGAATCAAATTTGAAAGG 58.315 36.000 23.91 14.52 41.13 3.11
2303 4038 7.928307 TTCATAGAGAAATGGTTCCAGAAAG 57.072 36.000 0.00 0.00 33.92 2.62
2473 4208 0.681564 AGTACCAGACAGCCTCTCGG 60.682 60.000 0.00 0.00 0.00 4.63
2487 4222 4.710865 AGGCTTAAGGAACACTAGAGTACC 59.289 45.833 4.29 0.00 0.00 3.34
2512 4250 4.444022 CCCTACATAGAACTGCAAGCAGAT 60.444 45.833 27.17 16.62 46.30 2.90
2513 4251 3.118629 CCCTACATAGAACTGCAAGCAGA 60.119 47.826 27.17 6.36 46.30 4.26
2522 4260 3.460825 TGCCTTTCCCCTACATAGAACT 58.539 45.455 0.00 0.00 0.00 3.01
2526 4264 7.445945 GCTATATATGCCTTTCCCCTACATAG 58.554 42.308 0.00 0.00 0.00 2.23
2750 4488 7.015098 ACAACCTGTAATCAACATGGAAATTCA 59.985 33.333 0.00 0.00 37.50 2.57
2869 4607 4.022589 GCATCACATGGAAAGGTCATATGG 60.023 45.833 2.13 0.00 0.00 2.74
2877 4615 1.822990 AGCAAGCATCACATGGAAAGG 59.177 47.619 0.00 0.00 0.00 3.11
2959 4699 7.582667 AAAATAGTTGTTACTCAAAGCCAGT 57.417 32.000 0.00 0.00 37.81 4.00
3412 5204 8.792633 CAATTAGTCCAACTCCATCAGTAAAAA 58.207 33.333 0.00 0.00 32.30 1.94
3441 5233 6.671190 TCAAACTAATCAGTTCTGTTGCATG 58.329 36.000 0.00 0.00 44.41 4.06
3583 5377 9.430623 TCACTCGAAATGAAAATTACAGTATGA 57.569 29.630 0.00 0.00 39.69 2.15
3778 5572 3.687698 AGTTGAAACTGCAAACGTAGTGT 59.312 39.130 0.00 0.00 38.47 3.55
3784 5578 3.497118 TGACAAGTTGAAACTGCAAACG 58.503 40.909 10.54 0.00 39.66 3.60
3785 5579 6.242829 CAAATGACAAGTTGAAACTGCAAAC 58.757 36.000 10.54 0.00 39.66 2.93
3791 5585 5.329035 AGTGCAAATGACAAGTTGAAACT 57.671 34.783 10.54 6.04 42.04 2.66
3809 5603 2.973224 CGACAACAACATGCTTTAGTGC 59.027 45.455 0.00 0.00 0.00 4.40
3876 5671 2.027377 ACCTGAGAGCATTGAAGGAGTG 60.027 50.000 0.00 0.00 0.00 3.51
3914 5709 1.608590 AGTTTTGACAAGATGGCACCG 59.391 47.619 0.00 0.00 33.32 4.94
4070 5867 6.479331 ACGCGGGTTTTATTTTTATGTTGTTT 59.521 30.769 12.47 0.00 0.00 2.83
4107 5904 5.104485 GGAACACAGATGGAGTTAATAGGGT 60.104 44.000 0.00 0.00 0.00 4.34
4185 5982 4.806640 AAAATAACCATTCCTGCAGTGG 57.193 40.909 17.88 17.88 38.96 4.00
4191 5988 4.892433 TGGCACAAAAATAACCATTCCTG 58.108 39.130 0.00 0.00 31.92 3.86
4234 6032 5.490139 AAAATAGTGATGCTGGTTCATCG 57.510 39.130 0.00 0.00 44.32 3.84
4335 6133 4.867047 CGAGTCAATACAGAAATCAGCAGT 59.133 41.667 0.00 0.00 0.00 4.40
4357 6155 3.171277 GCAAGCTAATAAACTTGTGCCG 58.829 45.455 4.83 0.00 44.12 5.69
4495 6293 8.941995 ATGTTAGTCCTCTTGTATCATAGCTA 57.058 34.615 0.00 0.00 0.00 3.32
4501 6299 6.850752 TGTGATGTTAGTCCTCTTGTATCA 57.149 37.500 0.00 0.00 0.00 2.15
4509 6307 7.094805 TGCAACTATTTTGTGATGTTAGTCCTC 60.095 37.037 0.00 0.00 0.00 3.71
4570 6368 3.762288 TCTAGTGTGTGGCTCGATAAAGT 59.238 43.478 0.00 0.00 0.00 2.66
4572 6370 3.130516 CCTCTAGTGTGTGGCTCGATAAA 59.869 47.826 0.00 0.00 0.00 1.40
4614 6412 2.580322 TGATGGAGAAGGTTGGGCAATA 59.420 45.455 0.00 0.00 0.00 1.90
4643 6441 4.942483 TGTACCAACGAGAAGAACCAAAAA 59.058 37.500 0.00 0.00 0.00 1.94
4672 6470 8.463930 CCTCTTGGCTTTGATACCATATTAAA 57.536 34.615 0.00 0.00 35.42 1.52
4775 6573 1.290955 CAACACCTGCATGGCTTGG 59.709 57.895 2.33 0.00 40.22 3.61
4777 6575 1.202927 ACTACAACACCTGCATGGCTT 60.203 47.619 0.00 0.00 40.22 4.35
4783 6581 4.224147 ACCACATATACTACAACACCTGCA 59.776 41.667 0.00 0.00 0.00 4.41
4786 6584 6.775708 ACAAACCACATATACTACAACACCT 58.224 36.000 0.00 0.00 0.00 4.00
5239 7045 9.849166 CATAATTTGGTTTTATGACCTACGTTT 57.151 29.630 0.00 0.00 38.68 3.60
5251 7057 8.410673 TGCAAGAGGTACATAATTTGGTTTTA 57.589 30.769 0.00 0.00 0.00 1.52
5465 7274 3.823304 AGACCTGAGAAAAATGGAACTGC 59.177 43.478 0.00 0.00 0.00 4.40
5471 7280 7.331026 TGTAGTGATAGACCTGAGAAAAATGG 58.669 38.462 0.00 0.00 0.00 3.16
5479 7288 4.037446 GGCTCTTGTAGTGATAGACCTGAG 59.963 50.000 0.00 0.00 0.00 3.35
5641 7450 2.995258 AGCAACAACAAACAGCAACAAG 59.005 40.909 0.00 0.00 0.00 3.16
5676 7485 4.957296 AGGTACGGGAATGAATCATGTAC 58.043 43.478 11.08 11.08 38.47 2.90
5800 7612 9.806448 ATCACTGATCTACTACTGTTCTCATAT 57.194 33.333 0.00 0.00 0.00 1.78
5806 7618 8.172352 ACCATATCACTGATCTACTACTGTTC 57.828 38.462 0.00 0.00 0.00 3.18
5948 7760 9.419297 TGTATTCATGTCAGTAAAACAGAGTAC 57.581 33.333 0.00 0.00 0.00 2.73
5991 7803 7.750229 TTGATGATGGAGAAGCAATATAACC 57.250 36.000 0.00 0.00 0.00 2.85
6090 7902 3.321111 CAGTGGTACTGGTACAACAGAGT 59.679 47.826 17.43 0.00 42.35 3.24
6160 7972 5.710513 ACACTAAGTACGGTGTTGTGATA 57.289 39.130 13.64 0.00 43.05 2.15
6177 7989 1.890489 TCGCAGGCTCTAACAACACTA 59.110 47.619 0.00 0.00 0.00 2.74
6194 8006 5.452302 GCAATGTTGTGATACAATAACTCGC 59.548 40.000 0.00 0.00 40.59 5.03
6217 8029 6.148480 GTCCACATCTCATAGGTCATAAATGC 59.852 42.308 0.00 0.00 0.00 3.56
6521 8337 7.865385 GTGCAATGGTACTTCTGTAAATTGAAA 59.135 33.333 12.82 3.20 37.27 2.69
6646 8462 6.346919 GCACGTATAAATGAGGCTATGTTCTG 60.347 42.308 0.00 0.00 0.00 3.02
6871 8689 6.480524 TGTCACAAATCGTTTCAAGATAGG 57.519 37.500 0.00 0.00 0.00 2.57
6884 8702 6.801539 TTGTAAGGTCAGATGTCACAAATC 57.198 37.500 0.00 0.00 0.00 2.17
6922 8740 0.690744 ACAAAAGTTGGCTGCCCCTT 60.691 50.000 17.53 14.99 34.12 3.95
7004 8822 6.891306 TTCTGAAATTCCCTAGAAGATGGA 57.109 37.500 0.00 0.00 34.86 3.41
7086 8904 7.094890 GCATTTCTCCAATGTATATGTCTGAGG 60.095 40.741 0.00 0.00 43.95 3.86
7292 9110 5.694910 TCCAACGAGACTGTTTTTAGATGTC 59.305 40.000 0.00 0.00 0.00 3.06
7310 9135 3.914364 GCTTGCTCTACAAATTTCCAACG 59.086 43.478 0.00 0.00 37.96 4.10
7313 9138 5.288804 GTTTGCTTGCTCTACAAATTTCCA 58.711 37.500 0.00 0.00 37.96 3.53
7353 9178 6.166982 AGTTAACATCTAAGAGTCACTTGGC 58.833 40.000 8.61 0.00 39.38 4.52
7641 9506 2.113860 TGCCCATCTTTACACAGCTC 57.886 50.000 0.00 0.00 0.00 4.09
7703 9568 9.906660 TCAATGATTACTGTTCAAAATAACCAC 57.093 29.630 0.00 0.00 0.00 4.16
7723 9588 6.038603 GCCAAAGCAAGTCTATATGTCAATGA 59.961 38.462 0.00 0.00 39.53 2.57
7758 9623 6.455360 TGGCATAACATCTCAAGAAATTCC 57.545 37.500 0.00 0.00 0.00 3.01
7833 9698 2.435372 AGTGTGGGCAGAAAGAAACA 57.565 45.000 0.00 0.00 0.00 2.83
7834 9699 2.952310 AGAAGTGTGGGCAGAAAGAAAC 59.048 45.455 0.00 0.00 0.00 2.78
7842 9707 1.233019 CTCAACAGAAGTGTGGGCAG 58.767 55.000 0.00 0.00 36.84 4.85
7883 9780 1.466866 CCTGCAACGCACAGATCATTG 60.467 52.381 0.00 0.00 37.32 2.82
8045 10030 1.003233 AGGAAGACTTCGCTTGCCC 60.003 57.895 9.08 0.00 36.96 5.36
8098 10083 5.984323 GCCTCTTACAGCATAAAGGTAGTAC 59.016 44.000 0.00 0.00 0.00 2.73
8234 10375 7.828717 TGAAAGAGAGGAACATAATTATGCACA 59.171 33.333 22.66 6.46 37.19 4.57
8254 10395 1.885887 CAACCGGCCAAAGATGAAAGA 59.114 47.619 0.00 0.00 0.00 2.52
8391 10532 3.556775 TGAACGTACCTTTTCAAACGAGG 59.443 43.478 0.23 0.00 38.64 4.63
8425 10567 0.598065 AACCTCGGCTTTCATTGCAC 59.402 50.000 0.00 0.00 0.00 4.57
8433 10575 2.631545 ACTACTACACAACCTCGGCTTT 59.368 45.455 0.00 0.00 0.00 3.51
8437 10579 1.271379 TGCACTACTACACAACCTCGG 59.729 52.381 0.00 0.00 0.00 4.63
8452 10594 1.871418 TGATTCTAGGGAGCTGCACT 58.129 50.000 7.79 4.47 0.00 4.40


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

AutoCloner maintained by Alex Coulton.