Multiple sequence alignment - TraesCS7A01G311100

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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 TraesCS7A01G311100 chr7A 100.000 6300 0 0 1531 7830 440356441 440350142 0.000000e+00 11635.0
1 TraesCS7A01G311100 chr7A 100.000 1210 0 0 1 1210 440357971 440356762 0.000000e+00 2235.0
2 TraesCS7A01G311100 chr7B 95.165 5398 188 35 2456 7830 384771036 384765689 0.000000e+00 8455.0
3 TraesCS7A01G311100 chr7B 92.118 1256 46 15 1 1210 384773534 384772286 0.000000e+00 1722.0
4 TraesCS7A01G311100 chr7B 94.290 613 26 4 1581 2184 384771931 384771319 0.000000e+00 929.0
5 TraesCS7A01G311100 chr7B 95.259 232 9 2 2222 2451 384771317 384771086 4.460000e-97 366.0
6 TraesCS7A01G311100 chr7D 95.244 3827 121 26 3906 7709 389461031 389457243 0.000000e+00 6002.0
7 TraesCS7A01G311100 chr7D 92.661 1240 57 17 1 1210 389465572 389464337 0.000000e+00 1755.0
8 TraesCS7A01G311100 chr7D 96.229 875 20 4 3019 3889 389462432 389461567 0.000000e+00 1421.0
9 TraesCS7A01G311100 chr7D 94.565 920 40 7 1537 2451 389463910 389462996 0.000000e+00 1413.0
10 TraesCS7A01G311100 chr7D 96.923 520 16 0 2460 2979 389462950 389462431 0.000000e+00 872.0
11 TraesCS7A01G311100 chr7D 93.985 133 8 0 7696 7828 389455156 389455024 1.330000e-47 202.0
12 TraesCS7A01G311100 chr2D 84.848 165 25 0 2460 2624 24931099 24930935 4.860000e-37 167.0
13 TraesCS7A01G311100 chr2D 84.783 92 12 2 2532 2621 506786395 506786304 3.010000e-14 91.6
14 TraesCS7A01G311100 chr5D 80.982 163 29 2 2460 2621 476935142 476935303 2.290000e-25 128.0
15 TraesCS7A01G311100 chr3B 78.889 180 30 7 2453 2628 682816076 682816251 1.790000e-21 115.0
16 TraesCS7A01G311100 chr2B 81.618 136 25 0 5911 6046 680044372 680044507 6.420000e-21 113.0
17 TraesCS7A01G311100 chr5A 77.838 185 28 6 5323 5506 566330527 566330699 1.390000e-17 102.0
18 TraesCS7A01G311100 chr6B 76.757 185 29 7 5323 5506 63617362 63617533 3.010000e-14 91.6


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 TraesCS7A01G311100 chr7A 440350142 440357971 7829 True 6935.000000 11635 100.0000 1 7830 2 chr7A.!!$R1 7829
1 TraesCS7A01G311100 chr7B 384765689 384773534 7845 True 2868.000000 8455 94.2080 1 7830 4 chr7B.!!$R1 7829
2 TraesCS7A01G311100 chr7D 389455024 389465572 10548 True 1944.166667 6002 94.9345 1 7828 6 chr7D.!!$R1 7827

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
123 125 1.135575 CAACTTGCTTGGAATCGAGGC 60.136 52.381 0.00 0.00 0.00 4.70 F
1720 1877 1.996191 ACTCGAGATCTTGCGCTTTTC 59.004 47.619 21.68 0.13 0.00 2.29 F
1921 2086 0.254178 ATCATTCGCTTGCTCTGGGT 59.746 50.000 0.00 0.00 0.00 4.51 F
2451 2622 0.630673 TAGGGCTGTTTGGATGGCAT 59.369 50.000 0.00 0.00 0.00 4.40 F
2452 2623 0.974010 AGGGCTGTTTGGATGGCATG 60.974 55.000 3.81 0.00 0.00 4.06 F
2454 2625 1.592743 GCTGTTTGGATGGCATGCA 59.407 52.632 18.30 18.30 0.00 3.96 F
3118 3334 2.032528 TTGTGGCCCTGCTCTTCG 59.967 61.111 0.00 0.00 0.00 3.79 F
3625 3845 2.096819 TGTTTGTTGCGACTTCTTGGTC 59.903 45.455 5.50 0.00 0.00 4.02 F
4789 5541 2.124411 ACCCACCTTACACACACTTCT 58.876 47.619 0.00 0.00 0.00 2.85 F
5755 6512 0.647410 CTGAAGCAGGTTCGCGTATG 59.353 55.000 5.77 1.96 38.09 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1909 0.813184 AAGTCGATTCGCCGGTCTTA 59.187 50.000 1.90 0.00 0.00 2.10 R
2811 3027 2.169179 GAAATGTGATCGCGACAAAGC 58.831 47.619 12.93 0.51 0.00 3.51 R
2818 3034 2.171567 CTTGCTTGAAATGTGATCGCG 58.828 47.619 0.00 0.00 0.00 5.87 R
3625 3845 2.871096 TTAGGCCCACAACTTACCAG 57.129 50.000 0.00 0.00 0.00 4.00 R
4020 4762 4.545610 TCCAACACTTCGAATCAAATTGC 58.454 39.130 0.00 0.00 0.00 3.56 R
4082 4824 4.586001 ACCTTGCATGAAGTGATGAAAAGT 59.414 37.500 0.00 0.00 0.00 2.66 R
4564 5314 0.892358 AGGACAACATGCTGCAGGTG 60.892 55.000 21.37 16.58 0.00 4.00 R
4954 5707 1.853963 ACCTGCCAAGTAGTCGAGAT 58.146 50.000 0.00 0.00 0.00 2.75 R
6624 7382 0.306533 GAACGAAGCGACTTGGCAAA 59.693 50.000 0.00 0.00 34.64 3.68 R
7356 8117 0.036875 TTCCACCACACACACACACA 59.963 50.000 0.00 0.00 0.00 3.72 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
62 64 4.653868 TGTAACATATTCACCAAACCCGT 58.346 39.130 0.00 0.00 0.00 5.28
84 86 3.390967 TCTCCATCGCCATATTTCTGGAA 59.609 43.478 0.00 0.00 38.69 3.53
102 104 1.769465 GAAGACCCTCCATACTTCCCC 59.231 57.143 0.00 0.00 34.54 4.81
122 124 2.907910 CAACTTGCTTGGAATCGAGG 57.092 50.000 0.00 0.00 0.00 4.63
123 125 1.135575 CAACTTGCTTGGAATCGAGGC 60.136 52.381 0.00 0.00 0.00 4.70
127 129 2.584608 CTTGGAATCGAGGCCCGT 59.415 61.111 12.46 0.00 39.75 5.28
193 196 3.249119 GGAGTAGGAAGCCTCCCAT 57.751 57.895 0.00 0.00 43.64 4.00
241 244 7.125792 TCAAGTAGTGGGAGATTTAGAATCC 57.874 40.000 0.00 0.00 0.00 3.01
434 450 9.262358 CCTTAAAGAAATATAGGAGTGCTACAC 57.738 37.037 0.00 0.00 34.10 2.90
435 451 9.817809 CTTAAAGAAATATAGGAGTGCTACACA 57.182 33.333 0.00 0.00 36.74 3.72
436 452 9.817809 TTAAAGAAATATAGGAGTGCTACACAG 57.182 33.333 0.00 0.00 36.74 3.66
437 453 6.412362 AGAAATATAGGAGTGCTACACAGG 57.588 41.667 0.00 0.00 36.74 4.00
438 454 6.136857 AGAAATATAGGAGTGCTACACAGGA 58.863 40.000 0.00 0.00 36.74 3.86
512 552 9.706529 ATCCTCAGCAGATTGATATATACACTA 57.293 33.333 0.00 0.00 0.00 2.74
533 573 6.986231 CACTATACAAGTATCATGTCAGGCAA 59.014 38.462 0.00 0.00 35.76 4.52
547 587 2.169144 TCAGGCAATGTCTCGTCATCAT 59.831 45.455 0.00 0.00 0.00 2.45
565 605 4.432115 CATCATATCGATTTGACGCTGACG 60.432 45.833 18.94 1.38 37.54 4.35
588 628 4.511454 GTGCTTCACAAGAGTGTTGACATA 59.489 41.667 7.07 0.00 46.01 2.29
590 630 5.764686 TGCTTCACAAGAGTGTTGACATATT 59.235 36.000 7.07 0.00 46.01 1.28
591 631 6.934083 TGCTTCACAAGAGTGTTGACATATTA 59.066 34.615 7.07 0.00 46.01 0.98
611 651 3.472283 AACTCTGATGCTGGCTCATAG 57.528 47.619 0.00 1.35 0.00 2.23
743 792 7.556275 TGAAACTTGAGATTCAGTACTGGTTTT 59.444 33.333 22.48 5.93 32.92 2.43
779 828 2.348998 GTGCAGTCACCTCCTGGG 59.651 66.667 0.00 0.00 37.24 4.45
782 831 2.930019 CAGTCACCTCCTGGGCCA 60.930 66.667 5.85 5.85 39.10 5.36
890 940 5.730550 TCTCTTCTCTCTAGACAGACAGAC 58.269 45.833 0.00 0.00 26.82 3.51
1698 1855 4.821589 CCCGGCGGCACTCTCTTC 62.822 72.222 23.20 0.00 0.00 2.87
1720 1877 1.996191 ACTCGAGATCTTGCGCTTTTC 59.004 47.619 21.68 0.13 0.00 2.29
1752 1909 7.510549 TTTGTCCTTTTCTGAATTCGAGATT 57.489 32.000 0.04 0.00 0.00 2.40
1766 1923 2.052157 CGAGATTAAGACCGGCGAATC 58.948 52.381 9.30 9.41 0.00 2.52
1778 1935 1.153353 GGCGAATCGACTTTTGGACA 58.847 50.000 6.91 0.00 0.00 4.02
1782 1947 3.364964 GCGAATCGACTTTTGGACATGTT 60.365 43.478 6.91 0.00 0.00 2.71
1783 1948 4.783242 CGAATCGACTTTTGGACATGTTT 58.217 39.130 0.00 0.00 0.00 2.83
1784 1949 4.846137 CGAATCGACTTTTGGACATGTTTC 59.154 41.667 0.00 0.00 0.00 2.78
1832 1997 6.293298 CCAATGCTCTATCTAATGCTGTTGAC 60.293 42.308 0.00 0.00 0.00 3.18
1921 2086 0.254178 ATCATTCGCTTGCTCTGGGT 59.746 50.000 0.00 0.00 0.00 4.51
2002 2167 3.094572 CCATTGGCAGAAAGATCAAGGT 58.905 45.455 0.00 0.00 0.00 3.50
2060 2225 1.819903 GGCTAGTTCGTCTCAAGGAGT 59.180 52.381 0.00 0.00 0.00 3.85
2124 2289 3.074687 CCTAGGGCTGGTAGATCTCTGTA 59.925 52.174 0.00 0.00 0.00 2.74
2126 2291 2.245028 AGGGCTGGTAGATCTCTGTACA 59.755 50.000 0.00 0.00 0.00 2.90
2128 2293 3.024547 GGCTGGTAGATCTCTGTACACA 58.975 50.000 0.00 0.00 0.00 3.72
2129 2294 3.067461 GGCTGGTAGATCTCTGTACACAG 59.933 52.174 0.00 2.84 45.08 3.66
2134 2301 5.416013 TGGTAGATCTCTGTACACAGTCTTG 59.584 44.000 0.00 0.19 44.12 3.02
2168 2337 9.522804 CTGTTTCTTTAGATACATAGACACCTC 57.477 37.037 3.97 0.00 35.90 3.85
2200 2369 3.444034 GCTTTTCACCCCAATAGTCCTTC 59.556 47.826 0.00 0.00 0.00 3.46
2201 2370 4.662278 CTTTTCACCCCAATAGTCCTTCA 58.338 43.478 0.00 0.00 0.00 3.02
2209 2378 3.614092 CCAATAGTCCTTCAGCATGTGT 58.386 45.455 0.00 0.00 37.40 3.72
2220 2389 2.639970 GCATGTGTGCCAACCAGTA 58.360 52.632 0.00 0.00 45.76 2.74
2253 2422 7.071414 GGCATTGTTTTTGCTTAATTTGTCTC 58.929 34.615 0.00 0.00 40.03 3.36
2347 2517 2.173569 AGAGCCTACAATGGGATTCACC 59.826 50.000 0.00 0.00 38.08 4.02
2385 2555 2.699954 CTTAGCTTTCCACGGTGATGT 58.300 47.619 10.28 0.00 0.00 3.06
2406 2576 6.000891 TGTTTAGCATGCTTGTTAGTGAAG 57.999 37.500 28.02 0.00 0.00 3.02
2451 2622 0.630673 TAGGGCTGTTTGGATGGCAT 59.369 50.000 0.00 0.00 0.00 4.40
2452 2623 0.974010 AGGGCTGTTTGGATGGCATG 60.974 55.000 3.81 0.00 0.00 4.06
2454 2625 1.592743 GCTGTTTGGATGGCATGCA 59.407 52.632 18.30 18.30 0.00 3.96
2733 2949 6.831868 AGAAAGGTAGGCAAGTGAAAGTAAAA 59.168 34.615 0.00 0.00 0.00 1.52
2801 3017 5.897250 ACCCATACCAATTTAGCCTTTAAGG 59.103 40.000 6.64 6.64 38.80 2.69
2811 3027 2.427506 AGCCTTTAAGGAAAGCTGTCG 58.572 47.619 16.18 0.00 40.76 4.35
2982 3198 5.277058 CGAGTATGCTTCAGCTTAATCAACC 60.277 44.000 17.29 0.00 42.23 3.77
3034 3250 5.842328 TGGTCGTTTCCCTTATGGTCTATAT 59.158 40.000 0.00 0.00 34.77 0.86
3100 3316 6.693315 AACCACATAATATTGGGAAAGTCG 57.307 37.500 0.00 0.00 37.18 4.18
3118 3334 2.032528 TTGTGGCCCTGCTCTTCG 59.967 61.111 0.00 0.00 0.00 3.79
3625 3845 2.096819 TGTTTGTTGCGACTTCTTGGTC 59.903 45.455 5.50 0.00 0.00 4.02
3732 3953 7.062957 CCATCTCAATAAATACCCCTGACTTT 58.937 38.462 0.00 0.00 0.00 2.66
3819 4040 9.017509 ACTACAGGTTAATTATATAGCGCAGTA 57.982 33.333 11.47 1.44 0.00 2.74
3901 4124 7.224297 ACTTTGTGTGTGGTCATATCTAACTT 58.776 34.615 0.00 0.00 0.00 2.66
3902 4125 7.173218 ACTTTGTGTGTGGTCATATCTAACTTG 59.827 37.037 0.00 0.00 0.00 3.16
3903 4126 6.353404 TGTGTGTGGTCATATCTAACTTGA 57.647 37.500 0.00 0.00 0.00 3.02
3904 4127 6.946340 TGTGTGTGGTCATATCTAACTTGAT 58.054 36.000 0.00 0.00 0.00 2.57
4020 4762 7.148918 CGAGCCAGACAAAAATCATTTACTTTG 60.149 37.037 0.00 0.00 35.39 2.77
4045 4787 6.974622 GCAATTTGATTCGAAGTGTTGGATAT 59.025 34.615 13.90 0.00 0.00 1.63
4046 4788 8.128582 GCAATTTGATTCGAAGTGTTGGATATA 58.871 33.333 13.90 0.00 0.00 0.86
4047 4789 9.655769 CAATTTGATTCGAAGTGTTGGATATAG 57.344 33.333 3.35 0.00 0.00 1.31
4048 4790 7.786178 TTTGATTCGAAGTGTTGGATATAGG 57.214 36.000 3.35 0.00 0.00 2.57
4050 4792 7.119709 TGATTCGAAGTGTTGGATATAGGAA 57.880 36.000 3.35 0.00 0.00 3.36
4051 4793 7.561251 TGATTCGAAGTGTTGGATATAGGAAA 58.439 34.615 3.35 0.00 0.00 3.13
4052 4794 7.494625 TGATTCGAAGTGTTGGATATAGGAAAC 59.505 37.037 3.35 0.00 0.00 2.78
4295 5041 3.431673 TGGTTCACATGCCTCATTACA 57.568 42.857 0.00 0.00 0.00 2.41
4480 5230 6.779860 AGCAGTAAAGGTTCTCCAAGAATTA 58.220 36.000 0.00 0.00 36.50 1.40
4788 5540 2.158871 TCACCCACCTTACACACACTTC 60.159 50.000 0.00 0.00 0.00 3.01
4789 5541 2.124411 ACCCACCTTACACACACTTCT 58.876 47.619 0.00 0.00 0.00 2.85
4796 5548 5.462398 CACCTTACACACACTTCTGTAGAAC 59.538 44.000 0.00 0.00 0.00 3.01
4804 5556 4.916249 CACACTTCTGTAGAACGACCTAAC 59.084 45.833 0.00 0.00 0.00 2.34
4820 5572 5.047235 CGACCTAACCATATTCTTCTAGGGG 60.047 48.000 0.00 0.00 31.92 4.79
4902 5654 4.766891 CACTGTAATGTCAACCCCTCAATT 59.233 41.667 0.00 0.00 0.00 2.32
4929 5681 8.621532 TGCACTTGAATATTTTGTAGTTCTCT 57.378 30.769 0.00 0.00 0.00 3.10
5118 5871 2.972348 AGAAACCACACCTCAGGTAGA 58.028 47.619 0.00 0.00 37.07 2.59
5123 5876 5.615925 AACCACACCTCAGGTAGATATTC 57.384 43.478 0.00 0.00 37.07 1.75
5165 5918 6.183360 ACGTGCAGGCGATTATTTTTAACATA 60.183 34.615 6.26 0.00 35.59 2.29
5271 6024 3.193479 AGGCAAAATTTAGTGCTGCTACC 59.807 43.478 13.16 0.00 40.70 3.18
5273 6026 4.415735 GCAAAATTTAGTGCTGCTACCTC 58.584 43.478 7.47 0.00 37.78 3.85
5321 6075 9.197694 CTATTGCTAGTTTCATGTATGTACCTC 57.802 37.037 0.00 0.00 0.00 3.85
5328 6082 8.008513 AGTTTCATGTATGTACCTCTATTCGT 57.991 34.615 0.00 0.00 0.00 3.85
5755 6512 0.647410 CTGAAGCAGGTTCGCGTATG 59.353 55.000 5.77 1.96 38.09 2.39
5831 6588 3.826729 TCTGCTTCAGAGTAAGTAGCACA 59.173 43.478 0.00 0.00 38.60 4.57
5940 6697 1.945394 CAGCTGATGGAACCTGCATAC 59.055 52.381 8.42 0.00 0.00 2.39
5966 6723 7.180322 AGACTACATTGATGTCACAGATCTT 57.820 36.000 0.00 0.00 41.97 2.40
6165 6922 6.793492 AGAAGAACATGCAAAGAGTTAGTC 57.207 37.500 0.00 0.00 0.00 2.59
6240 6998 7.725251 ACCATGTAAAGGTTATGCAATTATGG 58.275 34.615 0.00 0.00 35.33 2.74
6288 7046 1.106285 GTCCTGTCAAATCATGCCCC 58.894 55.000 0.00 0.00 0.00 5.80
6490 7248 2.383527 GGAAAGCCTGTCTGTCGCG 61.384 63.158 0.00 0.00 29.28 5.87
6495 7253 2.338620 CCTGTCTGTCGCGTGGAA 59.661 61.111 5.77 0.00 0.00 3.53
6532 7290 2.833121 CGGGGCTATGGGGCAAAC 60.833 66.667 0.00 0.00 42.84 2.93
6567 7325 4.496341 CGCAATCAATAACTCCGCTGAAAT 60.496 41.667 0.00 0.00 0.00 2.17
6605 7363 8.693625 GTTGATTCTGTAGTTAGTGGTATAGGT 58.306 37.037 0.00 0.00 0.00 3.08
6624 7382 4.615513 AGGTTCTTGGTGCTCTATACTCT 58.384 43.478 0.00 0.00 0.00 3.24
6981 7740 1.583451 CGGGCACATGAATTTCGCG 60.583 57.895 0.00 0.00 0.00 5.87
7013 7772 4.236935 GCGTCAAATTCATGTGTTCCAAT 58.763 39.130 0.00 0.00 0.00 3.16
7057 7816 2.291209 ATGAAGTGCATGGTGACCAA 57.709 45.000 9.06 0.00 36.95 3.67
7166 7925 5.212194 CCAAATCAGACGAACAAAAACGAT 58.788 37.500 0.00 0.00 0.00 3.73
7249 8008 4.083537 CCGCAAGTTAACAACAGCTTGATA 60.084 41.667 8.61 0.00 38.58 2.15
7263 8022 5.807520 ACAGCTTGATATCTGACTAAACACG 59.192 40.000 3.98 0.00 34.57 4.49
7349 8110 2.095853 GGTTTGTCTCTGTGTGTGTGTG 59.904 50.000 0.00 0.00 0.00 3.82
7350 8111 2.742053 GTTTGTCTCTGTGTGTGTGTGT 59.258 45.455 0.00 0.00 0.00 3.72
7351 8112 2.008752 TGTCTCTGTGTGTGTGTGTG 57.991 50.000 0.00 0.00 0.00 3.82
7352 8113 1.275010 TGTCTCTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
7353 8114 1.660607 GTCTCTGTGTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
7354 8115 1.275010 TCTCTGTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
7355 8116 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
7356 8117 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
7357 8118 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7358 8119 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7359 8120 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7360 8121 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7361 8122 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7362 8123 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7363 8124 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7364 8125 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7365 8126 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
7366 8127 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
7394 8155 6.989155 TGGAAACACGGATAAGGATATACT 57.011 37.500 0.00 0.00 33.40 2.12
7395 8156 6.989659 TGGAAACACGGATAAGGATATACTC 58.010 40.000 0.00 0.00 33.40 2.59
7396 8157 6.014840 TGGAAACACGGATAAGGATATACTCC 60.015 42.308 0.00 0.00 39.13 3.85
7501 8267 1.137675 GGCAAAGTACCTACCTACCCG 59.862 57.143 0.00 0.00 0.00 5.28
7559 8325 1.946081 CCCAATTGGTTGCCACAAAAC 59.054 47.619 22.91 0.00 33.90 2.43
7564 8330 2.957491 TGGTTGCCACAAAACAAGAG 57.043 45.000 0.00 0.00 0.00 2.85
7570 8336 0.594796 CCACAAAACAAGAGTGCGCC 60.595 55.000 4.18 0.00 32.09 6.53
7648 8422 8.528917 AACACATGTTTTCATTTCTGATGATG 57.471 30.769 0.00 0.00 38.64 3.07
7649 8423 7.663827 ACACATGTTTTCATTTCTGATGATGT 58.336 30.769 0.00 0.00 38.64 3.06
7650 8424 8.795513 ACACATGTTTTCATTTCTGATGATGTA 58.204 29.630 0.00 0.00 38.64 2.29
7651 8425 9.628746 CACATGTTTTCATTTCTGATGATGTAA 57.371 29.630 0.00 0.00 38.64 2.41
7666 8440 9.414295 CTGATGATGTAATTTCTTCTTTTTGCA 57.586 29.630 0.00 0.00 0.00 4.08
7703 8478 8.184192 TGCTTAAAACATACTCGTACTACTACC 58.816 37.037 0.00 0.00 0.00 3.18
7753 10628 7.669438 AAACATATTTTTGCGAGATGAATCG 57.331 32.000 0.00 0.00 45.48 3.34
7777 10652 3.062099 GGTGTAATAGTGTGCGATGTGTG 59.938 47.826 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 2.972021 TCCAGAAATATGGCGATGGAGA 59.028 45.455 0.00 0.00 40.41 3.71
84 86 0.029989 GGGGGAAGTATGGAGGGTCT 60.030 60.000 0.00 0.00 0.00 3.85
88 90 1.596496 AGTTGGGGGAAGTATGGAGG 58.404 55.000 0.00 0.00 0.00 4.30
122 124 1.147473 CTCAATTTTTGGCAACGGGC 58.853 50.000 0.00 0.00 43.74 6.13
123 125 1.147473 GCTCAATTTTTGGCAACGGG 58.853 50.000 0.00 0.00 42.51 5.28
127 129 3.465871 GGTGAAGCTCAATTTTTGGCAA 58.534 40.909 0.00 0.00 31.84 4.52
193 196 1.378762 GCAAGGTTGAGGTAGGGCA 59.621 57.895 0.00 0.00 0.00 5.36
241 244 2.370349 AGATGACACTCCTGGTACTCG 58.630 52.381 0.00 0.00 0.00 4.18
415 431 6.406692 TCCTGTGTAGCACTCCTATATTTC 57.593 41.667 0.90 0.00 35.11 2.17
434 450 6.369615 CCTCCAAAAATGCAAAATACTTCCTG 59.630 38.462 0.00 0.00 0.00 3.86
435 451 6.269769 TCCTCCAAAAATGCAAAATACTTCCT 59.730 34.615 0.00 0.00 0.00 3.36
436 452 6.463360 TCCTCCAAAAATGCAAAATACTTCC 58.537 36.000 0.00 0.00 0.00 3.46
437 453 7.154656 ACTCCTCCAAAAATGCAAAATACTTC 58.845 34.615 0.00 0.00 0.00 3.01
438 454 7.066307 ACTCCTCCAAAAATGCAAAATACTT 57.934 32.000 0.00 0.00 0.00 2.24
505 545 8.307483 GCCTGACATGATACTTGTATAGTGTAT 58.693 37.037 0.00 0.00 37.73 2.29
512 552 6.359804 ACATTGCCTGACATGATACTTGTAT 58.640 36.000 0.00 0.00 0.00 2.29
533 573 6.584184 GTCAAATCGATATGATGACGAGACAT 59.416 38.462 14.00 0.00 39.31 3.06
565 605 2.677836 TGTCAACACTCTTGTGAAGCAC 59.322 45.455 3.03 0.00 46.55 4.40
572 612 8.367911 TCAGAGTTAATATGTCAACACTCTTGT 58.632 33.333 0.00 0.00 39.15 3.16
588 628 3.920231 TGAGCCAGCATCAGAGTTAAT 57.080 42.857 0.00 0.00 0.00 1.40
590 630 4.218312 TCTATGAGCCAGCATCAGAGTTA 58.782 43.478 11.04 0.00 37.31 2.24
591 631 3.036819 TCTATGAGCCAGCATCAGAGTT 58.963 45.455 11.04 0.00 37.31 3.01
611 651 5.940470 TCTTTTCCTACCTTTCTCTTGCATC 59.060 40.000 0.00 0.00 0.00 3.91
652 696 5.394115 CCACCTACACTGCAAACTTTTCTTT 60.394 40.000 0.00 0.00 0.00 2.52
735 784 6.023603 TCTATCTCTCCACCTTAAAACCAGT 58.976 40.000 0.00 0.00 0.00 4.00
743 792 3.954904 GCACACTCTATCTCTCCACCTTA 59.045 47.826 0.00 0.00 0.00 2.69
779 828 3.316308 TGCTTTTCTTTCTCACTCTTGGC 59.684 43.478 0.00 0.00 0.00 4.52
782 831 7.254137 GTTTCTTGCTTTTCTTTCTCACTCTT 58.746 34.615 0.00 0.00 0.00 2.85
859 909 6.346096 TGTCTAGAGAGAAGAGAAGTAGAGC 58.654 44.000 0.00 0.00 31.96 4.09
890 940 1.143684 CCCTCTCTCTCCTCTCCTCTG 59.856 61.905 0.00 0.00 0.00 3.35
1530 1586 3.070018 ACAGTTCGAAGAGAAGCCAATG 58.930 45.455 0.00 0.00 39.95 2.82
1531 1587 3.409026 ACAGTTCGAAGAGAAGCCAAT 57.591 42.857 0.00 0.00 39.95 3.16
1532 1588 2.910688 ACAGTTCGAAGAGAAGCCAA 57.089 45.000 0.00 0.00 39.95 4.52
1533 1589 2.755650 GAACAGTTCGAAGAGAAGCCA 58.244 47.619 0.00 0.00 39.95 4.75
1547 1703 3.414549 AAAATCGCAAACACGAACAGT 57.585 38.095 0.00 0.00 46.59 3.55
1605 1762 0.834500 CGACGAGAGAAATCGAAGCG 59.165 55.000 2.78 0.61 45.56 4.68
1698 1855 1.354040 AAGCGCAAGATCTCGAGTTG 58.646 50.000 11.47 10.91 43.02 3.16
1720 1877 4.858935 TCAGAAAAGGACAAAGCGAAATG 58.141 39.130 0.00 0.00 0.00 2.32
1752 1909 0.813184 AAGTCGATTCGCCGGTCTTA 59.187 50.000 1.90 0.00 0.00 2.10
1766 1923 6.885735 AAAAAGAAACATGTCCAAAAGTCG 57.114 33.333 0.00 0.00 0.00 4.18
1832 1997 2.485038 GCATTGCAATTCCAAACAAGGG 59.515 45.455 9.83 0.00 0.00 3.95
2060 2225 7.743116 TTACAGGGACCATGTAAGAATTCTA 57.257 36.000 24.18 3.59 38.02 2.10
2128 2293 8.594550 TCTAAAGAAACAGTAATAGCCAAGACT 58.405 33.333 0.00 0.00 0.00 3.24
2129 2294 8.773404 TCTAAAGAAACAGTAATAGCCAAGAC 57.227 34.615 0.00 0.00 0.00 3.01
2157 2324 2.882761 CCATGGCAATGAGGTGTCTATG 59.117 50.000 1.41 0.00 35.67 2.23
2161 2330 0.682209 AGCCATGGCAATGAGGTGTC 60.682 55.000 37.18 4.41 44.88 3.67
2168 2337 1.676615 GGGTGAAAAGCCATGGCAATG 60.677 52.381 37.18 0.00 44.88 2.82
2209 2378 1.454104 CACCCACTACTGGTTGGCA 59.546 57.895 0.00 0.00 35.46 4.92
2220 2389 1.140652 CAAAAACAATGCCCACCCACT 59.859 47.619 0.00 0.00 0.00 4.00
2253 2422 0.109153 TCATGGGGCATGGATTCGAG 59.891 55.000 0.00 0.00 41.66 4.04
2331 2501 3.282021 CACCAGGTGAATCCCATTGTAG 58.718 50.000 15.35 0.00 35.23 2.74
2347 2517 1.527034 AGCATGCACTTGTACACCAG 58.473 50.000 21.98 0.00 0.00 4.00
2385 2555 5.046910 GCTTCACTAACAAGCATGCTAAA 57.953 39.130 23.00 5.84 44.87 1.85
2451 2622 1.202592 GCCATGATCCAAATGCATGCA 60.203 47.619 25.04 25.04 38.40 3.96
2452 2623 1.508632 GCCATGATCCAAATGCATGC 58.491 50.000 11.82 11.82 38.40 4.06
2454 2625 1.796017 TGGCCATGATCCAAATGCAT 58.204 45.000 0.00 0.00 0.00 3.96
2503 2719 4.912766 GCTACTACAGAATCACATAGCGTC 59.087 45.833 0.00 0.00 0.00 5.19
2710 2926 6.378848 TGTTTTACTTTCACTTGCCTACCTTT 59.621 34.615 0.00 0.00 0.00 3.11
2733 2949 8.565896 TCAGTTCAAATACTGCATCTAATTGT 57.434 30.769 0.00 0.00 44.10 2.71
2811 3027 2.169179 GAAATGTGATCGCGACAAAGC 58.831 47.619 12.93 0.51 0.00 3.51
2818 3034 2.171567 CTTGCTTGAAATGTGATCGCG 58.828 47.619 0.00 0.00 0.00 5.87
3034 3250 6.074648 ACTCCATCCCTATCAACAACAAAAA 58.925 36.000 0.00 0.00 0.00 1.94
3100 3316 2.328099 CGAAGAGCAGGGCCACAAC 61.328 63.158 6.18 0.00 0.00 3.32
3118 3334 8.703604 TTCAGAACAAATATACAGAGTGCTAC 57.296 34.615 0.00 0.00 0.00 3.58
3255 3471 9.685828 GACCTTTAATTTGTGTGCTATTAAACA 57.314 29.630 0.00 0.00 32.95 2.83
3625 3845 2.871096 TTAGGCCCACAACTTACCAG 57.129 50.000 0.00 0.00 0.00 4.00
3732 3953 8.536175 ACCAAATAGTTTTTCTTCAACAGGAAA 58.464 29.630 0.00 0.00 34.44 3.13
3983 4725 8.420374 TTTTTGTCTGGCTCGTCTATTAATAG 57.580 34.615 15.25 15.25 0.00 1.73
4020 4762 4.545610 TCCAACACTTCGAATCAAATTGC 58.454 39.130 0.00 0.00 0.00 3.56
4045 4787 9.485206 GAAGTTGATACACACTTTAGTTTCCTA 57.515 33.333 0.00 0.00 0.00 2.94
4046 4788 8.211629 AGAAGTTGATACACACTTTAGTTTCCT 58.788 33.333 0.00 0.00 0.00 3.36
4047 4789 8.283291 CAGAAGTTGATACACACTTTAGTTTCC 58.717 37.037 0.00 0.00 0.00 3.13
4048 4790 8.827677 ACAGAAGTTGATACACACTTTAGTTTC 58.172 33.333 0.00 0.00 0.00 2.78
4050 4792 8.732746 AACAGAAGTTGATACACACTTTAGTT 57.267 30.769 0.00 0.00 36.39 2.24
4082 4824 4.586001 ACCTTGCATGAAGTGATGAAAAGT 59.414 37.500 0.00 0.00 0.00 2.66
4480 5230 1.306997 TCTCCCAGGCTCCGGAAAT 60.307 57.895 5.23 0.00 0.00 2.17
4564 5314 0.892358 AGGACAACATGCTGCAGGTG 60.892 55.000 21.37 16.58 0.00 4.00
4724 5474 6.204688 GTGTCAAACTGTCAATAAGGTGATGA 59.795 38.462 0.00 0.00 0.00 2.92
4788 5540 7.040473 AGAATATGGTTAGGTCGTTCTACAG 57.960 40.000 0.00 0.00 0.00 2.74
4789 5541 7.341256 AGAAGAATATGGTTAGGTCGTTCTACA 59.659 37.037 0.00 0.00 0.00 2.74
4796 5548 5.047235 CCCCTAGAAGAATATGGTTAGGTCG 60.047 48.000 0.00 0.00 0.00 4.79
4804 5556 6.768381 GTGTCTTTTCCCCTAGAAGAATATGG 59.232 42.308 0.00 0.00 35.40 2.74
4820 5572 7.043961 AGGAAAGGAAATTGAGTGTCTTTTC 57.956 36.000 4.07 4.07 36.91 2.29
4858 5610 5.824624 AGTGCTCCATGGACTAATTACAATG 59.175 40.000 11.44 0.00 45.69 2.82
4859 5611 5.824624 CAGTGCTCCATGGACTAATTACAAT 59.175 40.000 11.44 0.00 45.78 2.71
4954 5707 1.853963 ACCTGCCAAGTAGTCGAGAT 58.146 50.000 0.00 0.00 0.00 2.75
5118 5871 9.737427 CACGTCTACAAGTCATCTTAAGAATAT 57.263 33.333 9.71 0.00 31.35 1.28
5123 5876 5.161358 TGCACGTCTACAAGTCATCTTAAG 58.839 41.667 0.00 0.00 32.07 1.85
5165 5918 3.697045 AGTCGCATACACTTCTAGAAGCT 59.303 43.478 28.64 17.81 41.99 3.74
5181 5934 4.523083 AGGCCATCTTAAAAATAGTCGCA 58.477 39.130 5.01 0.00 0.00 5.10
5259 6012 7.792032 AGTAAAATATTGAGGTAGCAGCACTA 58.208 34.615 0.00 0.00 0.00 2.74
5293 6047 8.765219 GGTACATACATGAAACTAGCAATAGTG 58.235 37.037 0.00 0.00 0.00 2.74
5294 6048 8.705594 AGGTACATACATGAAACTAGCAATAGT 58.294 33.333 0.00 0.00 0.00 2.12
5348 6102 6.834168 AAAATATCGGATGTTCCAACAAGT 57.166 33.333 0.00 0.00 43.03 3.16
5354 6108 7.889873 AATACCAAAAATATCGGATGTTCCA 57.110 32.000 0.00 0.00 35.91 3.53
5643 6398 5.772672 AGATATTCTTCCATGCTCTCGTAGT 59.227 40.000 0.00 0.00 0.00 2.73
5689 6444 6.012508 ACCTTCAATCCTGAAATGACTCCTAA 60.013 38.462 0.00 0.00 41.05 2.69
5739 6496 1.337823 ACTTCATACGCGAACCTGCTT 60.338 47.619 15.93 0.00 0.00 3.91
5755 6512 8.931385 ATTATAATCCAAACATGCACAACTTC 57.069 30.769 0.00 0.00 0.00 3.01
5831 6588 4.644685 ACTGATTGCACTTAAAACACAGGT 59.355 37.500 0.00 0.00 0.00 4.00
5940 6697 4.986622 TCTGTGACATCAATGTAGTCTCG 58.013 43.478 0.00 0.00 41.95 4.04
5966 6723 3.941573 TGCTTTCACATGAGCATCTACA 58.058 40.909 0.00 0.00 43.46 2.74
6010 6767 5.874261 GTGCCAACATTATAAATGCCAACTT 59.126 36.000 0.00 0.00 0.00 2.66
6081 6838 4.337836 TGTGTGAGCAAAGAATTAACTGCA 59.662 37.500 7.60 0.00 37.26 4.41
6165 6922 5.725362 AGAATACTCCTTTGGTTCTTCTCG 58.275 41.667 0.00 0.00 0.00 4.04
6271 7029 2.734755 TAGGGGCATGATTTGACAGG 57.265 50.000 0.00 0.00 33.62 4.00
6288 7046 4.405358 GGCCTGAATAGAGGAGATGGATAG 59.595 50.000 0.00 0.00 34.69 2.08
6353 7111 5.476945 GGTACTCAATTTTGATGTCAACCCT 59.523 40.000 0.00 0.00 36.46 4.34
6490 7248 0.317854 GCGACTTTTGCCACTTCCAC 60.318 55.000 0.00 0.00 0.00 4.02
6495 7253 1.577328 CGGATGCGACTTTTGCCACT 61.577 55.000 0.00 0.00 0.00 4.00
6517 7275 0.843984 TCTAGTTTGCCCCATAGCCC 59.156 55.000 0.00 0.00 0.00 5.19
6532 7290 9.232082 GAGTTATTGATTGCGAGCTATATCTAG 57.768 37.037 4.80 0.00 0.00 2.43
6567 7325 9.647797 AACTACAGAATCAACATGTATTAACGA 57.352 29.630 0.00 0.00 0.00 3.85
6605 7363 5.178797 GCAAAGAGTATAGAGCACCAAGAA 58.821 41.667 0.00 0.00 0.00 2.52
6624 7382 0.306533 GAACGAAGCGACTTGGCAAA 59.693 50.000 0.00 0.00 34.64 3.68
6953 7712 1.768275 TCATGTGCCCGGATACATCTT 59.232 47.619 17.31 0.00 35.46 2.40
6981 7740 7.003072 CACATGAATTTGACGCATTTTTACAC 58.997 34.615 0.00 0.00 0.00 2.90
7057 7816 4.387026 TTTTGTTCAGATGGAGGATGGT 57.613 40.909 0.00 0.00 0.00 3.55
7106 7865 8.417884 TGTAGAATTTTGAGGAAAACCGAAAAT 58.582 29.630 0.00 0.00 33.86 1.82
7114 7873 8.641541 AGCATTTCTGTAGAATTTTGAGGAAAA 58.358 29.630 0.00 0.00 35.52 2.29
7119 7878 7.025963 GGTCAGCATTTCTGTAGAATTTTGAG 58.974 38.462 0.00 0.00 43.32 3.02
7153 7912 3.733224 TGGCATTTCATCGTTTTTGTTCG 59.267 39.130 0.00 0.00 0.00 3.95
7166 7925 1.275856 GCTGATTTGGGTGGCATTTCA 59.724 47.619 0.00 0.00 0.00 2.69
7249 8008 5.479306 ACATAAGCACGTGTTTAGTCAGAT 58.521 37.500 25.55 9.89 0.00 2.90
7263 8022 3.545703 ACTGATTGCCCTACATAAGCAC 58.454 45.455 0.00 0.00 35.96 4.40
7349 8110 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
7350 8111 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
7351 8112 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
7352 8113 0.250510 ACCACACACACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
7353 8114 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
7354 8115 0.957888 CCACCACACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
7355 8116 0.675208 TCCACCACACACACACACAC 60.675 55.000 0.00 0.00 0.00 3.82
7356 8117 0.036875 TTCCACCACACACACACACA 59.963 50.000 0.00 0.00 0.00 3.72
7357 8118 1.135517 GTTTCCACCACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
7358 8119 1.169577 GTTTCCACCACACACACACA 58.830 50.000 0.00 0.00 0.00 3.72
7359 8120 1.135517 GTGTTTCCACCACACACACAC 60.136 52.381 0.00 0.00 43.52 3.82
7360 8121 1.169577 GTGTTTCCACCACACACACA 58.830 50.000 0.00 0.00 43.52 3.72
7361 8122 0.098025 CGTGTTTCCACCACACACAC 59.902 55.000 4.23 0.00 44.14 3.82
7362 8123 1.027255 CCGTGTTTCCACCACACACA 61.027 55.000 4.23 0.00 44.14 3.72
7363 8124 0.745128 TCCGTGTTTCCACCACACAC 60.745 55.000 4.23 0.00 44.14 3.82
7364 8125 0.181587 ATCCGTGTTTCCACCACACA 59.818 50.000 4.23 0.00 44.14 3.72
7365 8126 2.172851 TATCCGTGTTTCCACCACAC 57.827 50.000 0.00 0.00 41.08 3.82
7366 8127 2.551287 CCTTATCCGTGTTTCCACCACA 60.551 50.000 0.00 0.00 38.41 4.17
7387 8148 7.413657 GCTGTTCGAGTCATCTAGGAGTATATC 60.414 44.444 0.00 0.00 0.00 1.63
7391 8152 3.878103 GCTGTTCGAGTCATCTAGGAGTA 59.122 47.826 0.00 0.00 0.00 2.59
7392 8153 2.685897 GCTGTTCGAGTCATCTAGGAGT 59.314 50.000 0.00 0.00 0.00 3.85
7393 8154 2.685388 TGCTGTTCGAGTCATCTAGGAG 59.315 50.000 0.00 0.00 0.00 3.69
7394 8155 2.723273 TGCTGTTCGAGTCATCTAGGA 58.277 47.619 0.00 0.00 0.00 2.94
7395 8156 3.119316 AGTTGCTGTTCGAGTCATCTAGG 60.119 47.826 0.00 0.00 0.00 3.02
7396 8157 4.103365 AGTTGCTGTTCGAGTCATCTAG 57.897 45.455 0.00 0.00 0.00 2.43
7501 8267 2.061028 CAAAAAGAGAATTGCCCGCAC 58.939 47.619 0.00 0.00 0.00 5.34
7703 8478 7.543947 TGTCACATATTACATCTTTCTGCTG 57.456 36.000 0.00 0.00 0.00 4.41
7753 10628 1.257936 CATCGCACACTATTACACCGC 59.742 52.381 0.00 0.00 0.00 5.68
7777 10652 3.003378 GTGCACTCCTTCAGGTTAACAAC 59.997 47.826 10.32 0.00 36.34 3.32


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

AutoCloner maintained by Alex Coulton.