Multiple sequence alignment - TraesCS4B01G096600

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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 TraesCS4B01G096600 chr4B 100.000 7571 0 0 1 7571 100843715 100851285 0.000000e+00 13982.0
1 TraesCS4B01G096600 chr4B 95.455 44 1 1 7419 7462 401836334 401836376 1.360000e-07 69.4
2 TraesCS4B01G096600 chr4D 95.632 6433 199 34 798 7191 68421820 68428209 0.000000e+00 10248.0
3 TraesCS4B01G096600 chr4D 88.732 142 14 2 7393 7533 68428483 68428623 1.010000e-38 172.0
4 TraesCS4B01G096600 chr4A 94.283 1854 89 12 4954 6802 518827762 518829603 0.000000e+00 2820.0
5 TraesCS4B01G096600 chr4A 93.342 1577 65 23 1897 3459 518824542 518826092 0.000000e+00 2294.0
6 TraesCS4B01G096600 chr4A 93.026 1477 84 14 3456 4926 518826138 518827601 0.000000e+00 2139.0
7 TraesCS4B01G096600 chr4A 90.969 753 53 7 1550 2294 518823401 518824146 0.000000e+00 1000.0
8 TraesCS4B01G096600 chr4A 88.184 694 52 21 798 1465 518822493 518823182 0.000000e+00 800.0
9 TraesCS4B01G096600 chr4A 81.319 182 10 8 7011 7192 518829812 518829969 7.980000e-25 126.0
10 TraesCS4B01G096600 chr4A 89.474 76 4 2 6527 6602 524473158 524473087 8.090000e-15 93.5
11 TraesCS4B01G096600 chr7B 96.366 798 25 2 1 794 60343170 60343967 0.000000e+00 1310.0
12 TraesCS4B01G096600 chr1A 95.620 799 30 3 1 794 6294973 6295771 0.000000e+00 1277.0
13 TraesCS4B01G096600 chrUn 95.363 798 31 6 1 794 31580070 31579275 0.000000e+00 1264.0
14 TraesCS4B01G096600 chrUn 94.987 798 35 3 1 794 292875028 292875824 0.000000e+00 1247.0
15 TraesCS4B01G096600 chrUn 89.474 76 4 2 6527 6602 334308723 334308794 8.090000e-15 93.5
16 TraesCS4B01G096600 chrUn 94.595 37 2 0 7535 7571 260668538 260668502 2.950000e-04 58.4
17 TraesCS4B01G096600 chr6A 95.244 799 34 2 1 795 600121008 600121806 0.000000e+00 1262.0
18 TraesCS4B01G096600 chr6A 100.000 28 0 0 7544 7571 75913735 75913708 1.400000e-02 52.8
19 TraesCS4B01G096600 chr5A 95.113 798 35 2 1 794 565492669 565491872 0.000000e+00 1254.0
20 TraesCS4B01G096600 chr5A 85.906 298 42 0 6118 6415 214920290 214920587 1.230000e-82 318.0
21 TraesCS4B01G096600 chr5A 89.157 166 17 1 3454 3619 214917029 214917193 9.960000e-49 206.0
22 TraesCS4B01G096600 chr2A 94.737 798 37 3 1 794 677114216 677113420 0.000000e+00 1236.0
23 TraesCS4B01G096600 chr2A 94.486 798 39 3 1 794 677075366 677074570 0.000000e+00 1225.0
24 TraesCS4B01G096600 chr2B 94.500 800 40 2 1 796 416843318 416842519 0.000000e+00 1230.0
25 TraesCS4B01G096600 chr2B 94.595 37 2 0 7535 7571 22788551 22788515 2.950000e-04 58.4
26 TraesCS4B01G096600 chr5D 86.458 288 39 0 6128 6415 200645381 200645668 4.410000e-82 316.0
27 TraesCS4B01G096600 chr5D 88.554 166 18 1 3454 3619 200642011 200642175 4.630000e-47 200.0
28 TraesCS4B01G096600 chr5D 88.415 164 17 2 3214 3376 200641718 200641880 5.990000e-46 196.0
29 TraesCS4B01G096600 chr5B 86.111 288 40 0 6128 6415 211589094 211589381 2.050000e-80 311.0
30 TraesCS4B01G096600 chr5B 88.554 166 18 1 3454 3619 211585620 211585784 4.630000e-47 200.0
31 TraesCS4B01G096600 chr5B 88.415 164 17 2 3214 3376 211585327 211585489 5.990000e-46 196.0
32 TraesCS4B01G096600 chr6D 91.667 72 4 1 6531 6602 367992690 367992621 1.740000e-16 99.0
33 TraesCS4B01G096600 chr6D 94.595 37 2 0 7535 7571 320235511 320235475 2.950000e-04 58.4
34 TraesCS4B01G096600 chr3B 89.474 76 4 2 6527 6602 103902935 103902864 8.090000e-15 93.5
35 TraesCS4B01G096600 chr3B 91.892 37 3 0 7526 7562 808037005 808037041 1.400000e-02 52.8
36 TraesCS4B01G096600 chr6B 86.842 76 6 2 6527 6602 29737852 29737923 1.750000e-11 82.4
37 TraesCS4B01G096600 chr6B 100.000 28 0 0 7544 7571 711692424 711692397 1.400000e-02 52.8
38 TraesCS4B01G096600 chr1D 91.228 57 3 1 6546 6602 468225812 468225758 8.150000e-10 76.8
39 TraesCS4B01G096600 chr7A 94.595 37 2 0 7535 7571 513573797 513573833 2.950000e-04 58.4


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 TraesCS4B01G096600 chr4B 100843715 100851285 7570 False 13982.000000 13982 100.000000 1 7571 1 chr4B.!!$F1 7570
1 TraesCS4B01G096600 chr4D 68421820 68428623 6803 False 5210.000000 10248 92.182000 798 7533 2 chr4D.!!$F1 6735
2 TraesCS4B01G096600 chr4A 518822493 518829969 7476 False 1529.833333 2820 90.187167 798 7192 6 chr4A.!!$F1 6394
3 TraesCS4B01G096600 chr7B 60343170 60343967 797 False 1310.000000 1310 96.366000 1 794 1 chr7B.!!$F1 793
4 TraesCS4B01G096600 chr1A 6294973 6295771 798 False 1277.000000 1277 95.620000 1 794 1 chr1A.!!$F1 793
5 TraesCS4B01G096600 chrUn 31579275 31580070 795 True 1264.000000 1264 95.363000 1 794 1 chrUn.!!$R1 793
6 TraesCS4B01G096600 chrUn 292875028 292875824 796 False 1247.000000 1247 94.987000 1 794 1 chrUn.!!$F1 793
7 TraesCS4B01G096600 chr6A 600121008 600121806 798 False 1262.000000 1262 95.244000 1 795 1 chr6A.!!$F1 794
8 TraesCS4B01G096600 chr5A 565491872 565492669 797 True 1254.000000 1254 95.113000 1 794 1 chr5A.!!$R1 793
9 TraesCS4B01G096600 chr5A 214917029 214920587 3558 False 262.000000 318 87.531500 3454 6415 2 chr5A.!!$F1 2961
10 TraesCS4B01G096600 chr2A 677113420 677114216 796 True 1236.000000 1236 94.737000 1 794 1 chr2A.!!$R2 793
11 TraesCS4B01G096600 chr2A 677074570 677075366 796 True 1225.000000 1225 94.486000 1 794 1 chr2A.!!$R1 793
12 TraesCS4B01G096600 chr2B 416842519 416843318 799 True 1230.000000 1230 94.500000 1 796 1 chr2B.!!$R2 795
13 TraesCS4B01G096600 chr5D 200641718 200645668 3950 False 237.333333 316 87.809000 3214 6415 3 chr5D.!!$F1 3201
14 TraesCS4B01G096600 chr5B 211585327 211589381 4054 False 235.666667 311 87.693333 3214 6415 3 chr5B.!!$F1 3201

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
687 694 0.874607 GACGAGCGTTGGTGTCAAGT 60.875 55.000 0.00 0.0 32.92 3.16 F
1332 1340 0.331954 ACCCTACTTGCGAGAGGAGA 59.668 55.000 8.31 0.0 31.45 3.71 F
2521 3486 0.031178 CAGCTGAAAACCCTGCACAC 59.969 55.000 8.42 0.0 34.07 3.82 F
3397 4368 0.039256 CTTGTTCACATTGGTGGCCG 60.039 55.000 0.00 0.0 45.32 6.13 F
3410 4382 1.336795 GGTGGCCGGTCTTGAATTTTG 60.337 52.381 7.97 0.0 0.00 2.44 F
4952 6584 2.929398 GGATAAAATTGCCAGGTTTGCG 59.071 45.455 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 3486 0.392998 CTCCGAGTCCACCCCATTTG 60.393 60.000 0.00 0.0 0.00 2.32 R
2542 3507 1.625818 AGCTCATTTCCACCGAGAACT 59.374 47.619 0.00 0.0 0.00 3.01 R
3864 4889 0.107800 CACTGGCTCTGCACTGCTAT 60.108 55.000 1.98 0.0 0.00 2.97 R
4944 6443 1.904287 TTGCTGGATAACGCAAACCT 58.096 45.000 0.00 0.0 42.56 3.50 R
4996 6628 3.307410 CCCAGTAATAAGACCACTGCACA 60.307 47.826 0.00 0.0 38.67 4.57 R
6951 10120 0.179111 CGGGCGCTACTCATTCAGAA 60.179 55.000 7.64 0.0 0.00 3.02 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
131 134 7.571080 TTAGGTTTTTAGGTTGTTCATCGTT 57.429 32.000 0.00 0.00 0.00 3.85
247 250 3.281727 AACCAGTCTGTTCAAGCAAGA 57.718 42.857 0.00 0.00 0.00 3.02
646 653 2.467566 TCTTTTCTTCGGTGGCTACC 57.532 50.000 9.66 9.66 43.89 3.18
687 694 0.874607 GACGAGCGTTGGTGTCAAGT 60.875 55.000 0.00 0.00 32.92 3.16
729 736 5.182380 TCTTTTCAGTTTTGTCTTGTCGGTT 59.818 36.000 0.00 0.00 0.00 4.44
820 827 2.520069 ACAACAAATACGGCATTCCCA 58.480 42.857 0.00 0.00 0.00 4.37
865 872 3.214328 CCCCCAAATTCTCGTTCCTATG 58.786 50.000 0.00 0.00 0.00 2.23
1304 1312 0.400213 TGAGTTTCACGCCTGGGATT 59.600 50.000 0.00 0.00 0.00 3.01
1332 1340 0.331954 ACCCTACTTGCGAGAGGAGA 59.668 55.000 8.31 0.00 31.45 3.71
1447 1479 1.305213 TGGGCAGGGAAAATGGCTC 60.305 57.895 0.00 0.00 42.51 4.70
1479 1511 6.016360 TGTTATTGTCCAGTGAATTTGTCAGG 60.016 38.462 0.00 0.00 36.74 3.86
1521 1556 9.639601 TGTATAAGATTTTAGATAGACATGCGG 57.360 33.333 0.00 0.00 0.00 5.69
1534 1569 2.420022 GACATGCGGCTTTGTAAGATGT 59.580 45.455 0.00 0.00 0.00 3.06
1570 1736 3.389329 AGGTCATAGGTGCATAAGTCTGG 59.611 47.826 0.00 0.00 0.00 3.86
1593 1759 6.424812 TGGTGCATATCATCGAAACTGAATAG 59.575 38.462 0.00 0.00 0.00 1.73
1596 1762 6.073602 TGCATATCATCGAAACTGAATAGCAC 60.074 38.462 0.00 0.00 0.00 4.40
1624 1790 5.253330 CCAAGGCTCTCTTTGGTTGTATTA 58.747 41.667 0.00 0.00 32.41 0.98
1649 1815 2.671177 GCTGCACAGCGTACACTGG 61.671 63.158 15.05 5.60 45.29 4.00
1856 2026 9.490379 CTAAGGTTTTGTCTACTCTGTAATGTT 57.510 33.333 0.00 0.00 0.00 2.71
1946 2119 6.736110 ATTGCAATAGTTAAGCCCATGAAT 57.264 33.333 11.02 0.00 0.00 2.57
2033 2207 7.045416 TGAGTTGACGTATACTGCCATAAAAT 58.955 34.615 6.76 0.00 0.00 1.82
2051 2225 7.767198 CCATAAAATTTGCCATGAGAAAGATGT 59.233 33.333 0.00 0.00 0.00 3.06
2212 2387 1.331756 CACAGTGAACAAGTCAGCCAC 59.668 52.381 0.00 0.00 36.74 5.01
2223 2398 3.695830 AGTCAGCCACGGATCTTAAAA 57.304 42.857 0.00 0.00 0.00 1.52
2265 2440 5.843019 TTCTATGTCCTCTTTTGGGTCTT 57.157 39.130 0.00 0.00 0.00 3.01
2294 2469 0.976641 ATGGTGACCAGTGTGTCGAT 59.023 50.000 11.23 0.00 36.75 3.59
2295 2470 0.756294 TGGTGACCAGTGTGTCGATT 59.244 50.000 0.00 0.00 38.11 3.34
2296 2471 1.148310 GGTGACCAGTGTGTCGATTG 58.852 55.000 0.00 0.00 38.11 2.67
2297 2472 1.540363 GGTGACCAGTGTGTCGATTGT 60.540 52.381 0.00 0.00 38.11 2.71
2298 2473 1.792949 GTGACCAGTGTGTCGATTGTC 59.207 52.381 0.00 0.00 38.11 3.18
2299 2474 1.060713 GACCAGTGTGTCGATTGTCG 58.939 55.000 0.00 0.00 42.10 4.35
2364 3329 4.510038 ACTGAGAACATGTTTTGCCATC 57.490 40.909 13.36 0.00 0.00 3.51
2422 3387 5.915196 GCAGTACAAAATTTCAGAACCAGTC 59.085 40.000 0.00 0.00 0.00 3.51
2521 3486 0.031178 CAGCTGAAAACCCTGCACAC 59.969 55.000 8.42 0.00 34.07 3.82
2542 3507 0.546747 AATGGGGTGGACTCGGAGAA 60.547 55.000 12.86 0.00 34.09 2.87
2625 3590 4.305989 TCTTGTTTGCACATCCTTGTTC 57.694 40.909 0.00 0.00 32.34 3.18
2668 3635 7.656542 TGAATTGCTTAAATGCATGTTCTTTCA 59.343 29.630 0.00 0.55 42.96 2.69
2837 3804 9.675464 AAGATCCGTATTTGGTTAATTGTTCTA 57.325 29.630 0.00 0.00 0.00 2.10
2859 3828 7.483307 TCTATGTTGGCTCATATTTTTCTTGC 58.517 34.615 4.15 0.00 31.19 4.01
2895 3864 8.237811 ACTTTTGGTTCTGACATTCTTTGTAT 57.762 30.769 0.00 0.00 39.18 2.29
2919 3888 2.315720 ATTTCTTCCTTTGCCTGCCT 57.684 45.000 0.00 0.00 0.00 4.75
2992 3961 5.090139 TGAAATGGCCCATCTTCCTTTAAA 58.910 37.500 0.00 0.00 0.00 1.52
3006 3975 8.392372 TCTTCCTTTAAAGTTTTCTAGCCTTC 57.608 34.615 14.03 0.00 0.00 3.46
3155 4124 2.482721 GGTACGTGCTGCACTTATTTGT 59.517 45.455 28.04 19.52 31.34 2.83
3156 4125 2.686558 ACGTGCTGCACTTATTTGTG 57.313 45.000 28.04 13.70 40.62 3.33
3157 4126 2.217750 ACGTGCTGCACTTATTTGTGA 58.782 42.857 28.04 0.00 40.12 3.58
3158 4127 2.813754 ACGTGCTGCACTTATTTGTGAT 59.186 40.909 28.04 1.37 40.12 3.06
3159 4128 3.120199 ACGTGCTGCACTTATTTGTGATC 60.120 43.478 28.04 0.00 40.12 2.92
3160 4129 3.125829 CGTGCTGCACTTATTTGTGATCT 59.874 43.478 28.04 0.00 40.12 2.75
3161 4130 4.329801 CGTGCTGCACTTATTTGTGATCTA 59.670 41.667 28.04 0.00 40.12 1.98
3162 4131 5.563842 GTGCTGCACTTATTTGTGATCTAC 58.436 41.667 24.68 0.00 40.12 2.59
3397 4368 0.039256 CTTGTTCACATTGGTGGCCG 60.039 55.000 0.00 0.00 45.32 6.13
3410 4382 1.336795 GGTGGCCGGTCTTGAATTTTG 60.337 52.381 7.97 0.00 0.00 2.44
3496 4519 9.617523 ACTTTTCATTTTCAGATTCATTGGTTT 57.382 25.926 0.00 0.00 0.00 3.27
3631 4654 4.761235 TGAGTCACTTGTAAGTACCGAG 57.239 45.455 0.00 0.00 37.08 4.63
3798 4823 9.814899 ACATTACAAGAGTATTGAGAAGATGAG 57.185 33.333 4.13 0.00 35.92 2.90
3799 4824 8.763356 CATTACAAGAGTATTGAGAAGATGAGC 58.237 37.037 4.13 0.00 34.89 4.26
3837 4862 6.102615 TCCATGCAAGGGGTTAAATATCTAGT 59.897 38.462 8.36 0.00 39.14 2.57
4010 5035 3.005050 ACACTGGCATTTGATTGTGACTG 59.995 43.478 7.65 0.00 0.00 3.51
4399 5802 6.653320 TGTAAATCAGTTCATACACACTTCCC 59.347 38.462 0.00 0.00 0.00 3.97
4402 5805 5.241403 TCAGTTCATACACACTTCCCAAT 57.759 39.130 0.00 0.00 0.00 3.16
4636 6133 3.116395 AGGAATAGGAGATTGGGCTCTCT 60.116 47.826 2.73 0.00 41.23 3.10
4656 6153 7.220300 GCTCTCTGATTTGTAAAATGCATGAAG 59.780 37.037 0.00 0.00 0.00 3.02
4886 6385 3.003480 GCTGATCACTTCCCTAACACAC 58.997 50.000 0.00 0.00 0.00 3.82
4926 6425 3.955471 TCATTTCTTGCCAAGGTAGGAG 58.045 45.455 4.30 0.00 0.00 3.69
4944 6443 3.269381 AGGAGACCTGGATAAAATTGCCA 59.731 43.478 0.00 0.00 29.57 4.92
4952 6584 2.929398 GGATAAAATTGCCAGGTTTGCG 59.071 45.455 0.00 0.00 0.00 4.85
4996 6628 8.179509 TGTTAAAGTAGCTCTGTAGACTTCTT 57.820 34.615 0.00 0.00 30.98 2.52
5080 7927 9.962783 AAATTTCTGAAATTCTGAAGTGAGAAG 57.037 29.630 24.13 0.37 40.05 2.85
5495 8346 0.460459 GCGGCCTCTACTCAAGGAAC 60.460 60.000 0.00 0.00 35.83 3.62
5593 8557 5.070981 AGTTGATTCCTGAGTTTGAGAGTCA 59.929 40.000 0.00 0.00 36.31 3.41
5991 8955 6.198403 GCATTTTCATCGAGATGTACTTCGTA 59.802 38.462 12.22 0.88 39.72 3.43
6023 8987 8.391075 TCATTCTGGAACTACAAGGTAAAAAG 57.609 34.615 0.00 0.00 0.00 2.27
6480 9573 6.496338 GGTCTCTTTTGACCGTTATTTGAT 57.504 37.500 0.00 0.00 45.69 2.57
6482 9575 5.795441 GTCTCTTTTGACCGTTATTTGATGC 59.205 40.000 0.00 0.00 0.00 3.91
6529 9623 0.541863 CGGCTATCTGGGGTCAACTT 59.458 55.000 0.00 0.00 0.00 2.66
6859 10026 2.502142 TTGATGCAGTGCAGATTCCT 57.498 45.000 24.20 4.99 43.65 3.36
6901 10068 0.899720 AATGGGTTGCAGCATTCAGG 59.100 50.000 2.05 0.00 0.00 3.86
6966 10135 6.476706 TGATGTTACATTCTGAATGAGTAGCG 59.523 38.462 31.11 8.43 41.46 4.26
7008 10177 2.290896 CCAGTTTGAGATGTGCCCCTTA 60.291 50.000 0.00 0.00 0.00 2.69
7032 10201 3.383620 TGCTGGTTTTCATTTGCGATT 57.616 38.095 0.00 0.00 0.00 3.34
7098 10267 6.401047 AGCTTGCTGACGGTACTATATTTA 57.599 37.500 0.00 0.00 0.00 1.40
7153 10322 1.597797 CGGTGGCCATGTGCTGAATT 61.598 55.000 9.72 0.00 40.92 2.17
7181 10350 9.753669 GTTTTTGTAATACCAATAAATGCTTGC 57.246 29.630 0.00 0.00 0.00 4.01
7192 10361 7.148656 ACCAATAAATGCTTGCGTTATTTTCAC 60.149 33.333 0.16 0.00 0.00 3.18
7194 10363 8.382130 CAATAAATGCTTGCGTTATTTTCACAT 58.618 29.630 0.16 0.00 0.00 3.21
7210 10408 3.743521 TCACATCAGAGGGAAACTTGTG 58.256 45.455 0.00 0.00 35.49 3.33
7211 10409 3.136443 TCACATCAGAGGGAAACTTGTGT 59.864 43.478 0.00 0.00 35.63 3.72
7212 10410 4.346709 TCACATCAGAGGGAAACTTGTGTA 59.653 41.667 0.00 0.00 35.63 2.90
7213 10411 4.452455 CACATCAGAGGGAAACTTGTGTAC 59.548 45.833 0.00 0.00 0.00 2.90
7233 10431 3.963129 ACGTAACATTGGATCCCACATT 58.037 40.909 9.90 1.44 30.78 2.71
7237 10435 2.738743 ACATTGGATCCCACATTGGAC 58.261 47.619 9.90 0.00 40.96 4.02
7239 10437 1.079796 TTGGATCCCACATTGGACCA 58.920 50.000 9.90 0.00 40.96 4.02
7248 10446 0.810031 ACATTGGACCATAGACGCGC 60.810 55.000 5.73 0.00 0.00 6.86
7296 10495 3.055385 TCCCTGAAAACCTAACATCTCGG 60.055 47.826 0.00 0.00 0.00 4.63
7331 10530 2.495084 GTCTCAAGGGGATATTTCGGC 58.505 52.381 0.00 0.00 0.00 5.54
7348 10547 2.432456 CGCACGAGCTGGCTACAA 60.432 61.111 2.73 0.00 39.10 2.41
7349 10548 2.447887 CGCACGAGCTGGCTACAAG 61.448 63.158 2.73 0.00 39.10 3.16
7351 10550 1.355066 GCACGAGCTGGCTACAAGAC 61.355 60.000 0.00 0.00 37.91 3.01
7354 10553 1.070134 ACGAGCTGGCTACAAGACAAA 59.930 47.619 0.00 0.00 29.23 2.83
7355 10554 1.728971 CGAGCTGGCTACAAGACAAAG 59.271 52.381 0.00 0.00 29.23 2.77
7356 10555 1.466558 GAGCTGGCTACAAGACAAAGC 59.533 52.381 0.00 0.00 29.23 3.51
7357 10556 0.166814 GCTGGCTACAAGACAAAGCG 59.833 55.000 0.00 0.00 29.23 4.68
7358 10557 1.512926 CTGGCTACAAGACAAAGCGT 58.487 50.000 0.00 0.00 29.23 5.07
7359 10558 1.195448 CTGGCTACAAGACAAAGCGTG 59.805 52.381 0.00 0.00 29.23 5.34
7360 10559 1.202592 TGGCTACAAGACAAAGCGTGA 60.203 47.619 0.00 0.00 37.11 4.35
7365 10582 2.213499 ACAAGACAAAGCGTGAAGGAG 58.787 47.619 0.00 0.00 0.00 3.69
7387 10604 6.072508 GGAGCACAATGTGAGAAAGAATACAA 60.073 38.462 18.66 0.00 35.23 2.41
7401 10647 4.385825 AGAATACAAACGAGTTCTTGGCA 58.614 39.130 0.00 0.00 0.00 4.92
7402 10648 4.452455 AGAATACAAACGAGTTCTTGGCAG 59.548 41.667 0.00 0.00 0.00 4.85
7407 10653 1.080093 CGAGTTCTTGGCAGCGGTA 60.080 57.895 0.00 0.00 0.00 4.02
7410 10656 2.737359 CGAGTTCTTGGCAGCGGTAATA 60.737 50.000 0.00 0.00 0.00 0.98
7415 10661 0.107410 TTGGCAGCGGTAATAGTGGG 60.107 55.000 0.00 0.00 0.00 4.61
7431 10677 2.042433 AGTGGGCCAAGCTTAATTACCA 59.958 45.455 8.40 0.83 0.00 3.25
7433 10679 3.450817 GTGGGCCAAGCTTAATTACCAAT 59.549 43.478 8.40 0.00 0.00 3.16
7505 10752 9.092338 TGAATAATCCTATTATGGCAAGCAAAT 57.908 29.630 0.00 0.00 0.00 2.32
7509 10756 6.395426 TCCTATTATGGCAAGCAAATTCAG 57.605 37.500 0.00 0.00 0.00 3.02
7533 10780 4.082571 AGCAAAGTAAGCTAGGCAACAATG 60.083 41.667 0.00 0.00 41.32 2.82
7534 10781 4.321230 GCAAAGTAAGCTAGGCAACAATGT 60.321 41.667 0.00 0.00 41.41 2.71
7535 10782 5.106317 GCAAAGTAAGCTAGGCAACAATGTA 60.106 40.000 0.00 0.00 41.41 2.29
7536 10783 6.314784 CAAAGTAAGCTAGGCAACAATGTAC 58.685 40.000 0.00 0.00 41.41 2.90
7537 10784 5.422214 AGTAAGCTAGGCAACAATGTACT 57.578 39.130 0.00 0.00 41.41 2.73
7538 10785 5.420409 AGTAAGCTAGGCAACAATGTACTC 58.580 41.667 0.00 0.00 41.41 2.59
7539 10786 4.559862 AAGCTAGGCAACAATGTACTCT 57.440 40.909 0.00 0.00 41.41 3.24
7540 10787 4.130286 AGCTAGGCAACAATGTACTCTC 57.870 45.455 0.00 0.00 41.41 3.20
7541 10788 3.772025 AGCTAGGCAACAATGTACTCTCT 59.228 43.478 0.00 0.00 41.41 3.10
7542 10789 4.223923 AGCTAGGCAACAATGTACTCTCTT 59.776 41.667 0.00 0.00 41.41 2.85
7543 10790 4.938226 GCTAGGCAACAATGTACTCTCTTT 59.062 41.667 0.00 0.00 41.41 2.52
7544 10791 5.163814 GCTAGGCAACAATGTACTCTCTTTG 60.164 44.000 0.00 0.00 41.41 2.77
7545 10792 4.718961 AGGCAACAATGTACTCTCTTTGT 58.281 39.130 0.00 0.00 37.31 2.83
7546 10793 4.757149 AGGCAACAATGTACTCTCTTTGTC 59.243 41.667 0.00 0.00 35.61 3.18
7547 10794 4.757149 GGCAACAATGTACTCTCTTTGTCT 59.243 41.667 0.00 0.00 35.61 3.41
7548 10795 5.106908 GGCAACAATGTACTCTCTTTGTCTC 60.107 44.000 0.00 0.00 35.61 3.36
7549 10796 5.466728 GCAACAATGTACTCTCTTTGTCTCA 59.533 40.000 0.00 0.00 35.61 3.27
7550 10797 6.017934 GCAACAATGTACTCTCTTTGTCTCAA 60.018 38.462 0.00 0.00 35.61 3.02
7551 10798 7.467267 GCAACAATGTACTCTCTTTGTCTCAAA 60.467 37.037 0.00 0.00 35.61 2.69
7552 10799 8.397906 CAACAATGTACTCTCTTTGTCTCAAAA 58.602 33.333 0.00 0.00 35.61 2.44
7553 10800 8.682936 ACAATGTACTCTCTTTGTCTCAAAAT 57.317 30.769 0.00 0.00 32.77 1.82
7554 10801 9.778741 ACAATGTACTCTCTTTGTCTCAAAATA 57.221 29.630 0.00 0.00 32.77 1.40
7558 10805 9.261180 TGTACTCTCTTTGTCTCAAAATAAGTG 57.739 33.333 0.00 0.00 0.00 3.16
7559 10806 9.262358 GTACTCTCTTTGTCTCAAAATAAGTGT 57.738 33.333 10.44 9.87 0.00 3.55
7560 10807 8.371770 ACTCTCTTTGTCTCAAAATAAGTGTC 57.628 34.615 0.00 0.00 0.00 3.67
7561 10808 8.207545 ACTCTCTTTGTCTCAAAATAAGTGTCT 58.792 33.333 0.00 0.00 0.00 3.41
7562 10809 8.594881 TCTCTTTGTCTCAAAATAAGTGTCTC 57.405 34.615 0.00 0.00 0.00 3.36
7563 10810 8.204160 TCTCTTTGTCTCAAAATAAGTGTCTCA 58.796 33.333 0.00 0.00 0.00 3.27
7564 10811 8.731275 TCTTTGTCTCAAAATAAGTGTCTCAA 57.269 30.769 0.00 0.00 0.00 3.02
7565 10812 8.830580 TCTTTGTCTCAAAATAAGTGTCTCAAG 58.169 33.333 0.00 0.00 0.00 3.02
7566 10813 6.545504 TGTCTCAAAATAAGTGTCTCAAGC 57.454 37.500 0.00 0.00 0.00 4.01
7567 10814 6.291377 TGTCTCAAAATAAGTGTCTCAAGCT 58.709 36.000 0.00 0.00 0.00 3.74
7568 10815 6.767902 TGTCTCAAAATAAGTGTCTCAAGCTT 59.232 34.615 0.00 0.00 0.00 3.74
7569 10816 7.931407 TGTCTCAAAATAAGTGTCTCAAGCTTA 59.069 33.333 0.00 0.00 0.00 3.09
7570 10817 8.439286 GTCTCAAAATAAGTGTCTCAAGCTTAG 58.561 37.037 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 77 1.999048 AAAATCGATCCACACGCGTA 58.001 45.000 13.44 0.00 0.00 4.42
131 134 1.872388 TCGTCATCACCGAAGCAAAA 58.128 45.000 0.00 0.00 0.00 2.44
529 536 2.159179 ACCAAAAGTGAAGCCCTTGT 57.841 45.000 0.00 0.00 0.00 3.16
553 560 1.880646 GCTTTGCGGACCTCCAAAGTA 60.881 52.381 23.94 2.26 45.91 2.24
729 736 9.843334 AAAGAACAAAGTACAAATCACGTAAAA 57.157 25.926 0.00 0.00 0.00 1.52
796 803 4.151512 GGGAATGCCGTATTTGTTGTTTTG 59.848 41.667 0.00 0.00 33.83 2.44
820 827 3.444818 TTTTGCGGGGAGGTGCCTT 62.445 57.895 0.00 0.00 36.66 4.35
1332 1340 2.762234 CCTCTACGCCGCGAAGACT 61.762 63.158 21.79 0.00 0.00 3.24
1447 1479 4.562082 TCACTGGACAATAACACGGTTAG 58.438 43.478 0.00 0.00 0.00 2.34
1479 1511 5.360144 TCTTATACAGGAGTCAACACCTAGC 59.640 44.000 0.00 0.00 35.12 3.42
1519 1554 2.223340 GCCATCACATCTTACAAAGCCG 60.223 50.000 0.00 0.00 0.00 5.52
1521 1556 4.357142 CATGCCATCACATCTTACAAAGC 58.643 43.478 0.00 0.00 0.00 3.51
1570 1736 6.073602 TGCTATTCAGTTTCGATGATATGCAC 60.074 38.462 0.00 0.00 0.00 4.57
1593 1759 1.127343 AGAGAGCCTTGGGATAGTGC 58.873 55.000 0.00 0.00 0.00 4.40
1649 1815 9.988815 ACTCCATAACTAAACTATCACATGATC 57.011 33.333 0.00 0.00 36.05 2.92
1903 2075 6.015095 TGCAATTAATTACCATGTGTCCAACA 60.015 34.615 0.00 0.00 44.79 3.33
1904 2076 6.393990 TGCAATTAATTACCATGTGTCCAAC 58.606 36.000 0.00 0.00 0.00 3.77
1906 2078 6.596309 TTGCAATTAATTACCATGTGTCCA 57.404 33.333 0.00 0.00 0.00 4.02
2009 2183 6.897259 TTTTATGGCAGTATACGTCAACTC 57.103 37.500 0.00 0.00 0.00 3.01
2033 2207 6.409524 AAGAAACATCTTTCTCATGGCAAA 57.590 33.333 0.00 0.00 44.59 3.68
2084 2259 1.544724 ACATTTGGGATTGTGGACCG 58.455 50.000 0.00 0.00 0.00 4.79
2422 3387 2.863809 ACCTTGTTTACCCAGAGCTTG 58.136 47.619 0.00 0.00 0.00 4.01
2521 3486 0.392998 CTCCGAGTCCACCCCATTTG 60.393 60.000 0.00 0.00 0.00 2.32
2542 3507 1.625818 AGCTCATTTCCACCGAGAACT 59.374 47.619 0.00 0.00 0.00 3.01
2837 3804 6.290294 AGCAAGAAAAATATGAGCCAACAT 57.710 33.333 0.00 0.00 0.00 2.71
2859 3828 5.067674 TCAGAACCAAAAGTCACATCCAAAG 59.932 40.000 0.00 0.00 0.00 2.77
2919 3888 5.491070 CAGATCATCTAGGTGGTTTCACAA 58.509 41.667 2.43 0.00 45.32 3.33
2992 3961 3.334583 TGATGCGAAGGCTAGAAAACT 57.665 42.857 0.00 0.00 40.82 2.66
3006 3975 7.191551 ACTCACTTGATTATCAAAATGATGCG 58.808 34.615 16.81 10.93 37.70 4.73
3142 4111 7.783090 ATCAGTAGATCACAAATAAGTGCAG 57.217 36.000 0.00 0.00 39.35 4.41
3157 4126 7.952671 TCCGCTAATGTTTAAGATCAGTAGAT 58.047 34.615 12.50 0.00 35.24 1.98
3158 4127 7.342769 TCCGCTAATGTTTAAGATCAGTAGA 57.657 36.000 12.50 0.00 35.24 2.59
3159 4128 8.328864 GTTTCCGCTAATGTTTAAGATCAGTAG 58.671 37.037 0.00 0.00 35.99 2.57
3160 4129 7.279313 GGTTTCCGCTAATGTTTAAGATCAGTA 59.721 37.037 0.00 0.00 0.00 2.74
3161 4130 6.093633 GGTTTCCGCTAATGTTTAAGATCAGT 59.906 38.462 0.00 0.00 0.00 3.41
3162 4131 6.316390 AGGTTTCCGCTAATGTTTAAGATCAG 59.684 38.462 0.00 0.00 0.00 2.90
3397 4368 7.386025 CCAAAATCCTTCTCAAAATTCAAGACC 59.614 37.037 0.00 0.00 0.00 3.85
3410 4382 3.486383 TGACACCACCAAAATCCTTCTC 58.514 45.455 0.00 0.00 0.00 2.87
3631 4654 7.092716 ACATGATTTAACAGAAATGCCAAGAC 58.907 34.615 0.00 0.00 0.00 3.01
3798 4823 3.159472 TGCATGGAAATGATGGATAGGC 58.841 45.455 0.00 0.00 0.00 3.93
3799 4824 4.219944 CCTTGCATGGAAATGATGGATAGG 59.780 45.833 13.33 0.00 0.00 2.57
3864 4889 0.107800 CACTGGCTCTGCACTGCTAT 60.108 55.000 1.98 0.00 0.00 2.97
3868 4893 1.531423 AATTCACTGGCTCTGCACTG 58.469 50.000 0.00 0.00 0.00 3.66
4010 5035 8.742188 CGTTGTGTGTATTCAAATATTTATGCC 58.258 33.333 0.00 0.00 0.00 4.40
4394 5797 3.967332 AATCTTTGGCACATTGGGAAG 57.033 42.857 0.00 0.00 39.30 3.46
4636 6133 8.339344 TCTCTCTTCATGCATTTTACAAATCA 57.661 30.769 0.00 0.00 0.00 2.57
4656 6153 7.938715 AGATGGCATGAAATTACAATTCTCTC 58.061 34.615 3.81 0.00 0.00 3.20
4714 6211 3.976654 CTCTAGGGAAATCAATCTGGGGA 59.023 47.826 0.00 0.00 0.00 4.81
4944 6443 1.904287 TTGCTGGATAACGCAAACCT 58.096 45.000 0.00 0.00 42.56 3.50
4996 6628 3.307410 CCCAGTAATAAGACCACTGCACA 60.307 47.826 0.00 0.00 38.67 4.57
5080 7927 5.120674 GCTGAAATGGTAAATGTGCCTTTTC 59.879 40.000 18.84 18.84 45.78 2.29
5224 8072 9.340695 CATAATATTTCAGTTGCGTGAAAAAGA 57.659 29.630 11.39 3.27 46.73 2.52
5339 8187 8.709308 ACTAATGGAAACTCATACTAGCTGAAT 58.291 33.333 0.00 0.00 0.00 2.57
5839 8803 2.533318 GAGCACCACTCCAGTTTCG 58.467 57.895 0.00 0.00 39.75 3.46
5991 8955 6.656693 CCTTGTAGTTCCAGAATGAAGTGAAT 59.343 38.462 0.00 0.00 39.69 2.57
6023 8987 4.787598 CAAAGTTCACCAACATACTGCTC 58.212 43.478 0.00 0.00 34.60 4.26
6095 9188 6.541641 AGAAGCTGTCAACTATCCATCAATTC 59.458 38.462 0.00 0.00 0.00 2.17
6108 9201 1.683385 AGGGCAAAAGAAGCTGTCAAC 59.317 47.619 0.00 0.00 0.00 3.18
6480 9573 5.830991 ACCTAAATAAAAACAGTGTCAGGCA 59.169 36.000 0.00 0.00 0.00 4.75
6482 9575 6.016276 AGCACCTAAATAAAAACAGTGTCAGG 60.016 38.462 0.00 0.00 0.00 3.86
6529 9623 6.419484 TCTGTAGATTCTCCTGACAAACAA 57.581 37.500 0.00 0.00 0.00 2.83
6859 10026 1.204146 GGGGCACATCTAGGTTCAGA 58.796 55.000 0.00 0.00 0.00 3.27
6901 10068 9.562583 TTGCTTTTATATGACATAAAACGGAAC 57.437 29.630 0.00 0.00 32.17 3.62
6939 10108 7.493971 GCTACTCATTCAGAATGTAACATCAGT 59.506 37.037 20.49 16.40 39.87 3.41
6951 10120 0.179111 CGGGCGCTACTCATTCAGAA 60.179 55.000 7.64 0.00 0.00 3.02
6966 10135 0.887387 TGGCTAACAGTTCAACGGGC 60.887 55.000 0.00 0.00 0.00 6.13
7008 10177 2.865551 CGCAAATGAAAACCAGCAAACT 59.134 40.909 0.00 0.00 0.00 2.66
7032 10201 2.494059 GTTGGCTAACAGTTCTGCTCA 58.506 47.619 8.23 5.29 36.78 4.26
7135 10304 0.609662 AAATTCAGCACATGGCCACC 59.390 50.000 8.16 0.00 46.50 4.61
7139 10308 4.035441 ACAAAAACAAATTCAGCACATGGC 59.965 37.500 0.00 0.00 45.30 4.40
7181 10350 6.149474 AGTTTCCCTCTGATGTGAAAATAACG 59.851 38.462 0.00 0.00 0.00 3.18
7192 10361 3.679980 CGTACACAAGTTTCCCTCTGATG 59.320 47.826 0.00 0.00 0.00 3.07
7194 10363 2.696707 ACGTACACAAGTTTCCCTCTGA 59.303 45.455 0.00 0.00 0.00 3.27
7210 10408 3.864243 TGTGGGATCCAATGTTACGTAC 58.136 45.455 15.23 0.00 34.18 3.67
7211 10409 4.764050 ATGTGGGATCCAATGTTACGTA 57.236 40.909 15.23 0.00 34.18 3.57
7212 10410 3.644966 ATGTGGGATCCAATGTTACGT 57.355 42.857 15.23 0.00 34.18 3.57
7213 10411 3.066621 CCAATGTGGGATCCAATGTTACG 59.933 47.826 15.23 0.00 34.18 3.18
7233 10431 4.201679 CCGCGCGTCTATGGTCCA 62.202 66.667 29.95 0.00 0.00 4.02
7237 10435 0.170339 TATCATCCGCGCGTCTATGG 59.830 55.000 29.95 12.39 0.00 2.74
7239 10437 1.202302 CCATATCATCCGCGCGTCTAT 60.202 52.381 29.95 16.07 0.00 1.98
7248 10446 5.677319 AACTATACCACCCATATCATCCG 57.323 43.478 0.00 0.00 0.00 4.18
7277 10476 3.334691 TGCCGAGATGTTAGGTTTTCAG 58.665 45.455 0.00 0.00 0.00 3.02
7296 10495 0.176910 GAGACCCTAGTTGCCTCTGC 59.823 60.000 0.00 0.00 38.26 4.26
7313 10512 1.512926 CGCCGAAATATCCCCTTGAG 58.487 55.000 0.00 0.00 0.00 3.02
7331 10530 2.432456 TTGTAGCCAGCTCGTGCG 60.432 61.111 3.48 0.00 45.42 5.34
7337 10536 1.528129 GCTTTGTCTTGTAGCCAGCT 58.472 50.000 0.00 0.00 0.00 4.24
7344 10543 3.390135 CTCCTTCACGCTTTGTCTTGTA 58.610 45.455 0.00 0.00 0.00 2.41
7346 10545 1.069636 GCTCCTTCACGCTTTGTCTTG 60.070 52.381 0.00 0.00 0.00 3.02
7347 10546 1.230324 GCTCCTTCACGCTTTGTCTT 58.770 50.000 0.00 0.00 0.00 3.01
7348 10547 0.106708 TGCTCCTTCACGCTTTGTCT 59.893 50.000 0.00 0.00 0.00 3.41
7349 10548 0.235926 GTGCTCCTTCACGCTTTGTC 59.764 55.000 0.00 0.00 0.00 3.18
7351 10550 0.662619 TTGTGCTCCTTCACGCTTTG 59.337 50.000 0.00 0.00 39.73 2.77
7354 10553 0.250467 ACATTGTGCTCCTTCACGCT 60.250 50.000 0.00 0.00 39.73 5.07
7355 10554 0.110056 CACATTGTGCTCCTTCACGC 60.110 55.000 3.43 0.00 39.73 5.34
7356 10555 1.462283 CTCACATTGTGCTCCTTCACG 59.538 52.381 12.04 0.00 39.73 4.35
7357 10556 2.771089 TCTCACATTGTGCTCCTTCAC 58.229 47.619 12.04 0.00 37.48 3.18
7358 10557 3.490439 TTCTCACATTGTGCTCCTTCA 57.510 42.857 12.04 0.00 32.98 3.02
7359 10558 4.067896 TCTTTCTCACATTGTGCTCCTTC 58.932 43.478 12.04 0.00 32.98 3.46
7360 10559 4.090761 TCTTTCTCACATTGTGCTCCTT 57.909 40.909 12.04 0.00 32.98 3.36
7365 10582 6.086765 CGTTTGTATTCTTTCTCACATTGTGC 59.913 38.462 12.04 0.00 32.98 4.57
7387 10604 1.961277 CCGCTGCCAAGAACTCGTT 60.961 57.895 0.00 0.00 0.00 3.85
7401 10647 0.180406 CTTGGCCCACTATTACCGCT 59.820 55.000 0.00 0.00 0.00 5.52
7402 10648 1.444917 GCTTGGCCCACTATTACCGC 61.445 60.000 0.00 0.00 0.00 5.68
7407 10653 4.893524 GGTAATTAAGCTTGGCCCACTATT 59.106 41.667 9.86 0.00 0.00 1.73
7410 10656 2.042433 TGGTAATTAAGCTTGGCCCACT 59.958 45.455 9.86 0.00 0.00 4.00
7415 10661 6.761242 CCCTAAAATTGGTAATTAAGCTTGGC 59.239 38.462 9.86 0.00 0.00 4.52
7456 10702 9.973450 TTCATCTAGTTGCATATCTAAGAACTC 57.027 33.333 0.00 0.00 0.00 3.01
7498 10745 5.010415 AGCTTACTTTGCTCTGAATTTGCTT 59.990 36.000 0.00 0.00 35.67 3.91
7505 10752 3.007940 TGCCTAGCTTACTTTGCTCTGAA 59.992 43.478 0.00 0.00 41.46 3.02
7509 10756 3.074412 TGTTGCCTAGCTTACTTTGCTC 58.926 45.455 0.00 0.00 41.46 4.26
7533 10780 9.262358 ACACTTATTTTGAGACAAAGAGAGTAC 57.738 33.333 0.00 0.00 0.00 2.73
7534 10781 9.477484 GACACTTATTTTGAGACAAAGAGAGTA 57.523 33.333 0.00 0.00 0.00 2.59
7535 10782 8.207545 AGACACTTATTTTGAGACAAAGAGAGT 58.792 33.333 0.00 0.00 0.00 3.24
7536 10783 8.600449 AGACACTTATTTTGAGACAAAGAGAG 57.400 34.615 0.00 0.00 0.00 3.20
7537 10784 8.204160 TGAGACACTTATTTTGAGACAAAGAGA 58.796 33.333 0.00 0.00 0.00 3.10
7538 10785 8.370493 TGAGACACTTATTTTGAGACAAAGAG 57.630 34.615 0.00 0.00 0.00 2.85
7539 10786 8.731275 TTGAGACACTTATTTTGAGACAAAGA 57.269 30.769 0.00 0.00 0.00 2.52
7540 10787 7.589221 GCTTGAGACACTTATTTTGAGACAAAG 59.411 37.037 0.00 0.00 0.00 2.77
7541 10788 7.283127 AGCTTGAGACACTTATTTTGAGACAAA 59.717 33.333 0.00 0.00 0.00 2.83
7542 10789 6.767902 AGCTTGAGACACTTATTTTGAGACAA 59.232 34.615 0.00 0.00 0.00 3.18
7543 10790 6.291377 AGCTTGAGACACTTATTTTGAGACA 58.709 36.000 0.00 0.00 0.00 3.41
7544 10791 6.793492 AGCTTGAGACACTTATTTTGAGAC 57.207 37.500 0.00 0.00 0.00 3.36
7545 10792 8.539770 CTAAGCTTGAGACACTTATTTTGAGA 57.460 34.615 9.86 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.