Multiple sequence alignment - TraesCS3D01G006900

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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 TraesCS3D01G006900 chr3D 100.000 4545 0 0 1 4545 2452430 2447886 0.000000e+00 8394.0
1 TraesCS3D01G006900 chr3D 95.050 101 5 0 3966 4066 160515366 160515466 4.990000e-35 159.0
2 TraesCS3D01G006900 chr3D 100.000 38 0 0 4784 4821 2447647 2447610 2.410000e-08 71.3
3 TraesCS3D01G006900 chr3D 76.296 135 22 5 334 468 141402852 141402728 4.030000e-06 63.9
4 TraesCS3D01G006900 chrUn 92.158 3494 183 30 518 3967 270455742 270452296 0.000000e+00 4850.0
5 TraesCS3D01G006900 chrUn 92.158 3494 183 30 518 3967 270464006 270460560 0.000000e+00 4850.0
6 TraesCS3D01G006900 chrUn 92.158 3494 183 30 518 3967 280684601 280681155 0.000000e+00 4850.0
7 TraesCS3D01G006900 chrUn 90.476 462 30 8 61 521 270456221 270455773 8.930000e-167 597.0
8 TraesCS3D01G006900 chrUn 90.476 462 30 8 61 521 270464485 270464037 8.930000e-167 597.0
9 TraesCS3D01G006900 chrUn 90.476 462 30 8 61 521 280685080 280684632 8.930000e-167 597.0
10 TraesCS3D01G006900 chr3A 94.438 2787 101 18 1190 3967 1620652 1623393 0.000000e+00 4239.0
11 TraesCS3D01G006900 chr3A 94.549 587 14 1 518 1104 1619730 1620298 0.000000e+00 891.0
12 TraesCS3D01G006900 chr3A 91.414 396 24 6 1 386 1619201 1619596 7.100000e-148 534.0
13 TraesCS3D01G006900 chr3A 84.386 570 56 18 3963 4502 706783288 706782722 3.300000e-146 529.0
14 TraesCS3D01G006900 chr3A 94.366 71 3 1 908 977 719359174 719359244 1.830000e-19 108.0
15 TraesCS3D01G006900 chr3B 90.550 2783 182 36 1237 3967 3261928 3259175 0.000000e+00 3607.0
16 TraesCS3D01G006900 chr3B 88.664 247 14 3 518 750 3262617 3262371 6.100000e-74 289.0
17 TraesCS3D01G006900 chr3B 85.106 141 9 3 1105 1244 3262020 3261891 3.030000e-27 134.0
18 TraesCS3D01G006900 chr3B 100.000 34 0 0 4788 4821 29956425 29956392 4.030000e-06 63.9
19 TraesCS3D01G006900 chr2B 79.879 2485 322 98 1573 3970 131585923 131583530 0.000000e+00 1655.0
20 TraesCS3D01G006900 chr2B 87.791 172 19 2 1269 1439 131586104 131585934 2.940000e-47 200.0
21 TraesCS3D01G006900 chr2B 90.667 75 7 0 881 955 677963080 677963154 3.070000e-17 100.0
22 TraesCS3D01G006900 chr2B 97.297 37 1 0 4785 4821 23637779 23637815 4.030000e-06 63.9
23 TraesCS3D01G006900 chr2B 97.222 36 1 0 4785 4820 697546232 697546197 1.450000e-05 62.1
24 TraesCS3D01G006900 chr2D 83.218 1013 129 21 2886 3871 80037540 80036542 0.000000e+00 891.0
25 TraesCS3D01G006900 chr2D 84.729 203 28 2 1237 1439 80039004 80038805 2.940000e-47 200.0
26 TraesCS3D01G006900 chr2D 100.000 86 0 0 3966 4051 615386791 615386876 4.990000e-35 159.0
27 TraesCS3D01G006900 chr2D 84.536 97 15 0 2632 2728 294515877 294515781 3.970000e-16 97.1
28 TraesCS3D01G006900 chr2A 83.283 993 118 30 2889 3850 80618240 80617265 0.000000e+00 870.0
29 TraesCS3D01G006900 chr2A 78.974 975 142 35 1898 2860 80619157 80618234 1.480000e-169 606.0
30 TraesCS3D01G006900 chr2A 88.372 172 18 2 1269 1439 80619702 80619532 6.320000e-49 206.0
31 TraesCS3D01G006900 chr4A 90.476 315 25 5 3963 4276 528650100 528650410 1.250000e-110 411.0
32 TraesCS3D01G006900 chr5A 76.991 452 66 27 1575 1998 690644529 690644088 1.750000e-54 224.0
33 TraesCS3D01G006900 chr5A 76.991 452 66 27 1575 1998 698851779 698852220 1.750000e-54 224.0
34 TraesCS3D01G006900 chr5A 92.208 77 3 3 4439 4512 580281216 580281140 6.600000e-19 106.0
35 TraesCS3D01G006900 chr6A 89.011 182 16 2 3966 4143 72982356 72982175 6.280000e-54 222.0
36 TraesCS3D01G006900 chr6A 89.404 151 10 6 4127 4276 72976629 72976484 8.240000e-43 185.0
37 TraesCS3D01G006900 chr4D 96.040 101 4 0 3966 4066 113026462 113026562 1.070000e-36 165.0
38 TraesCS3D01G006900 chr4D 88.636 132 14 1 3966 4097 373590976 373590846 4.990000e-35 159.0
39 TraesCS3D01G006900 chr4D 98.851 87 1 0 3966 4052 40842654 40842568 6.460000e-34 156.0
40 TraesCS3D01G006900 chr4D 100.000 35 0 0 4784 4818 338364078 338364112 1.120000e-06 65.8
41 TraesCS3D01G006900 chr4B 96.939 98 3 0 881 978 323786718 323786815 1.070000e-36 165.0
42 TraesCS3D01G006900 chr5D 91.429 105 5 1 3966 4066 524326951 524326847 1.810000e-29 141.0
43 TraesCS3D01G006900 chr1D 93.220 59 3 1 910 967 468052264 468052322 8.600000e-13 86.1
44 TraesCS3D01G006900 chr1D 90.164 61 5 1 908 967 468051012 468051072 1.440000e-10 78.7
45 TraesCS3D01G006900 chr7D 100.000 37 0 0 4784 4820 7604992 7604956 8.660000e-08 69.4
46 TraesCS3D01G006900 chr7B 97.143 35 1 0 4785 4819 377325585 377325551 5.210000e-05 60.2
47 TraesCS3D01G006900 chr1B 97.143 35 1 0 4785 4819 128819329 128819295 5.210000e-05 60.2
48 TraesCS3D01G006900 chr1B 97.143 35 1 0 4785 4819 635433699 635433733 5.210000e-05 60.2


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 TraesCS3D01G006900 chr3D 2447610 2452430 4820 True 4232.650000 8394 100.000000 1 4821 2 chr3D.!!$R2 4820
1 TraesCS3D01G006900 chrUn 270452296 270456221 3925 True 2723.500000 4850 91.317000 61 3967 2 chrUn.!!$R1 3906
2 TraesCS3D01G006900 chrUn 270460560 270464485 3925 True 2723.500000 4850 91.317000 61 3967 2 chrUn.!!$R2 3906
3 TraesCS3D01G006900 chrUn 280681155 280685080 3925 True 2723.500000 4850 91.317000 61 3967 2 chrUn.!!$R3 3906
4 TraesCS3D01G006900 chr3A 1619201 1623393 4192 False 1888.000000 4239 93.467000 1 3967 3 chr3A.!!$F2 3966
5 TraesCS3D01G006900 chr3A 706782722 706783288 566 True 529.000000 529 84.386000 3963 4502 1 chr3A.!!$R1 539
6 TraesCS3D01G006900 chr3B 3259175 3262617 3442 True 1343.333333 3607 88.106667 518 3967 3 chr3B.!!$R2 3449
7 TraesCS3D01G006900 chr2B 131583530 131586104 2574 True 927.500000 1655 83.835000 1269 3970 2 chr2B.!!$R2 2701
8 TraesCS3D01G006900 chr2D 80036542 80039004 2462 True 545.500000 891 83.973500 1237 3871 2 chr2D.!!$R2 2634
9 TraesCS3D01G006900 chr2A 80617265 80619702 2437 True 560.666667 870 83.543000 1269 3850 3 chr2A.!!$R1 2581

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
919 977 0.466555 TAGTTGCCCAGGCGTTTGTT 60.467 50.0 3.83 0.00 45.51 2.83 F
2031 2611 1.126488 AGCTAGCTAGGCATGCAAGA 58.874 50.0 17.69 2.38 33.16 3.02 F
2978 3599 0.036105 TGCCACGCTTCAGTGATGAT 60.036 50.0 10.08 0.00 44.43 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2615 0.178068 GACCCTGGCGCTAATTCAGA 59.822 55.0 7.64 0.0 0.00 3.27 R
3533 4196 0.322546 GGTTGGTCCATCCCTGTCAC 60.323 60.0 7.68 0.0 35.97 3.67 R
4372 5065 0.034896 TCTCCCCTTTTCTCGTGTGC 59.965 55.0 0.00 0.0 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
55 57 9.314501 GTCAAACGATCTTACATTTCTTTACAC 57.685 33.333 0.00 0.00 0.00 2.90
80 84 9.436957 ACAGAGTATTTTCTAATGTGAAACGAT 57.563 29.630 0.00 0.00 42.39 3.73
238 248 6.438763 CGATGGTGCTTTCTAAAGAAAAAGT 58.561 36.000 6.64 0.00 42.72 2.66
278 288 4.087892 CTCACCACTCCGGGCCAG 62.088 72.222 4.39 0.00 40.22 4.85
290 300 2.436109 GGCCAGTGACATGTGGGT 59.564 61.111 1.15 0.00 34.06 4.51
293 303 1.371183 CCAGTGACATGTGGGTCGT 59.629 57.895 1.15 0.00 40.72 4.34
359 370 4.051922 GGAAGAAGTGACCGTATATGCAG 58.948 47.826 0.00 0.00 0.00 4.41
386 397 8.826710 GCATAGACAAGTTATGTTACTGCAATA 58.173 33.333 0.00 0.00 44.12 1.90
392 403 9.950680 ACAAGTTATGTTACTGCAATATAATGC 57.049 29.630 5.79 5.79 42.58 3.56
405 416 6.420306 TGCAATATAATGCCGTATTTTGCAAG 59.580 34.615 21.45 0.00 46.31 4.01
412 423 3.984633 TGCCGTATTTTGCAAGTTTTAGC 59.015 39.130 0.00 1.44 33.87 3.09
424 435 9.810545 TTTGCAAGTTTTAGCACTAAACTAAAT 57.189 25.926 0.00 0.00 41.05 1.40
425 436 9.810545 TTGCAAGTTTTAGCACTAAACTAAATT 57.189 25.926 0.00 0.00 41.05 1.82
426 437 9.243637 TGCAAGTTTTAGCACTAAACTAAATTG 57.756 29.630 10.12 5.94 38.89 2.32
427 438 9.458374 GCAAGTTTTAGCACTAAACTAAATTGA 57.542 29.630 13.50 0.00 38.89 2.57
473 484 6.426587 ACTGCCACTGATATTACCTTTTCAT 58.573 36.000 0.00 0.00 0.00 2.57
495 506 5.712217 TGTATTCATTAGTTTCGAAGCCG 57.288 39.130 8.51 0.00 37.07 5.52
620 664 5.460419 CGAACGGGAGAAAAATCTCATCTAG 59.540 44.000 8.01 0.00 38.44 2.43
690 748 6.500684 ACAAATACTAAGCACATCCAACAG 57.499 37.500 0.00 0.00 0.00 3.16
913 971 2.750237 GGGTTAGTTGCCCAGGCG 60.750 66.667 3.83 0.00 45.40 5.52
919 977 0.466555 TAGTTGCCCAGGCGTTTGTT 60.467 50.000 3.83 0.00 45.51 2.83
960 1018 4.135153 CTCCAGTCCGGCGTGAGG 62.135 72.222 6.01 2.09 33.14 3.86
1196 1661 2.317609 ACGCACACGATGAAGCACC 61.318 57.895 0.00 0.00 43.93 5.01
1784 2298 8.850027 TAATGAAGAACATAGGCTTCGAGGCC 62.850 46.154 29.84 29.84 44.35 5.19
1845 2385 7.069702 CAGGTATATATGTGCCATGATCTCTCT 59.930 40.741 9.20 0.00 0.00 3.10
1846 2386 7.069702 AGGTATATATGTGCCATGATCTCTCTG 59.930 40.741 9.20 0.00 0.00 3.35
1865 2407 1.579932 CCAGCTGCAGCAGTTTCAG 59.420 57.895 38.24 15.05 45.16 3.02
1893 2435 7.169158 TCAAAAGAGTTTTTCATGGAAGTGT 57.831 32.000 0.00 0.00 34.34 3.55
1927 2490 8.688747 ATGAAATTCAATTCTAGATGGGACTC 57.311 34.615 0.00 0.00 0.00 3.36
1928 2491 7.632861 TGAAATTCAATTCTAGATGGGACTCA 58.367 34.615 0.00 0.00 0.00 3.41
1984 2547 5.061853 ACAGGCTCATAGATTACATGCTTG 58.938 41.667 0.00 0.00 33.36 4.01
2014 2578 3.268023 ACTGGAATTGCTACACCTAGC 57.732 47.619 0.00 0.00 45.19 3.42
2020 2600 4.281182 GGAATTGCTACACCTAGCTAGCTA 59.719 45.833 22.85 22.85 45.20 3.32
2021 2601 5.461032 AATTGCTACACCTAGCTAGCTAG 57.539 43.478 35.39 35.39 45.20 3.42
2029 2609 2.827800 CTAGCTAGCTAGGCATGCAA 57.172 50.000 34.95 10.46 41.58 4.08
2030 2610 2.686235 CTAGCTAGCTAGGCATGCAAG 58.314 52.381 34.95 15.82 41.58 4.01
2031 2611 1.126488 AGCTAGCTAGGCATGCAAGA 58.874 50.000 17.69 2.38 33.16 3.02
2032 2612 1.487976 AGCTAGCTAGGCATGCAAGAA 59.512 47.619 17.69 7.22 33.16 2.52
2033 2613 1.872313 GCTAGCTAGGCATGCAAGAAG 59.128 52.381 22.10 16.20 0.00 2.85
2034 2614 1.872313 CTAGCTAGGCATGCAAGAAGC 59.128 52.381 21.36 20.05 45.96 3.86
2035 2615 0.255318 AGCTAGGCATGCAAGAAGCT 59.745 50.000 21.36 21.84 45.94 3.74
2038 2618 1.941294 CTAGGCATGCAAGAAGCTCTG 59.059 52.381 21.36 0.00 45.94 3.35
2046 2626 2.674852 TGCAAGAAGCTCTGAATTAGCG 59.325 45.455 0.00 0.00 44.87 4.26
2075 2655 9.682465 AGGGTCCAGATTTCTAGTTTAATTAAC 57.318 33.333 0.00 0.00 36.99 2.01
2152 2742 2.104859 CACTGGCACTCCATCAGCG 61.105 63.158 0.00 0.00 42.51 5.18
2203 2801 9.049523 CATAGTGTAAGCATTTCATACAGTGAT 57.950 33.333 0.00 0.00 34.50 3.06
2547 3155 6.378848 AGGTAAGACTGACTGAAGATTACCTC 59.621 42.308 18.34 0.00 42.78 3.85
2581 3189 6.634805 TCTCACTTGAAGAGTCACATATTCC 58.365 40.000 0.00 0.00 36.10 3.01
2660 3276 3.756082 ATAGCATCACCAAAAGGGGAA 57.244 42.857 0.00 0.00 42.91 3.97
2769 3385 2.620627 CCACCTTGGATGGTAAACCCTC 60.621 54.545 0.00 0.00 40.96 4.30
2828 3449 6.005583 AGTTTAGATTGCAACACATGTCTG 57.994 37.500 0.00 0.00 0.00 3.51
2974 3595 1.891919 GGTTGCCACGCTTCAGTGA 60.892 57.895 0.00 0.00 44.43 3.41
2975 3596 1.237285 GGTTGCCACGCTTCAGTGAT 61.237 55.000 0.00 0.00 44.43 3.06
2978 3599 0.036105 TGCCACGCTTCAGTGATGAT 60.036 50.000 10.08 0.00 44.43 2.45
3087 3708 1.004918 ACGCCTGTCAGTTACCAGC 60.005 57.895 0.00 0.00 0.00 4.85
3459 4107 7.658167 TGAAAACGGTACTCAACATCTCAAATA 59.342 33.333 0.00 0.00 0.00 1.40
3507 4169 9.871238 ACAAATTACTACTTGTCGTTCTCATAT 57.129 29.630 0.00 0.00 29.80 1.78
3533 4196 8.573035 TGGACATGAATGATCAATGTTATGATG 58.427 33.333 11.78 3.66 40.08 3.07
3970 4635 9.381033 GTAGTTTCTTTTCCCCTTCTTATCTAC 57.619 37.037 0.00 0.00 0.00 2.59
3999 4664 2.339769 AGAAGTTGCTCCCCACTACTT 58.660 47.619 0.00 0.00 36.12 2.24
4006 4671 3.039011 TGCTCCCCACTACTTCCTATTC 58.961 50.000 0.00 0.00 0.00 1.75
4027 4692 0.250424 CTCACCATGCACACTGTCCA 60.250 55.000 0.00 0.00 0.00 4.02
4050 4715 3.177600 GCGATGTGCCACGTCATT 58.822 55.556 16.77 0.00 33.83 2.57
4067 4732 6.847792 CACGTCATTCTATATTGACATGCAAC 59.152 38.462 0.00 0.00 41.85 4.17
4080 4745 4.518211 TGACATGCAACATGTACACATCAA 59.482 37.500 12.87 0.00 33.61 2.57
4082 4747 3.534524 TGCAACATGTACACATCAACG 57.465 42.857 0.00 0.00 33.61 4.10
4083 4748 3.134458 TGCAACATGTACACATCAACGA 58.866 40.909 0.00 0.00 33.61 3.85
4091 4756 0.606130 ACACATCAACGATGCAGCCA 60.606 50.000 0.00 0.00 43.15 4.75
4093 4758 1.061411 CATCAACGATGCAGCCACG 59.939 57.895 0.00 6.76 33.17 4.94
4094 4759 1.375908 ATCAACGATGCAGCCACGT 60.376 52.632 7.93 7.93 41.97 4.49
4097 4762 2.317609 AACGATGCAGCCACGTCAC 61.318 57.895 13.01 0.00 39.31 3.67
4109 4774 1.129251 CCACGTCACACTCATGCATTC 59.871 52.381 0.00 0.00 0.00 2.67
4113 4778 0.697658 TCACACTCATGCATTCCCCA 59.302 50.000 0.00 0.00 0.00 4.96
4114 4779 1.285667 TCACACTCATGCATTCCCCAT 59.714 47.619 0.00 0.00 0.00 4.00
4116 4781 2.882761 CACACTCATGCATTCCCCATAG 59.117 50.000 0.00 0.00 0.00 2.23
4140 4805 3.691342 CACCTCCTCGGGCGTGAA 61.691 66.667 4.89 0.00 36.97 3.18
4143 4808 0.974010 ACCTCCTCGGGCGTGAATTA 60.974 55.000 0.00 0.00 36.97 1.40
4146 4811 2.135933 CTCCTCGGGCGTGAATTAATC 58.864 52.381 0.00 0.00 0.00 1.75
4147 4812 0.859232 CCTCGGGCGTGAATTAATCG 59.141 55.000 0.00 0.00 0.00 3.34
4162 4827 9.869844 GTGAATTAATCGATAATGAAGACCAAG 57.130 33.333 0.00 0.00 34.41 3.61
4163 4828 9.613428 TGAATTAATCGATAATGAAGACCAAGT 57.387 29.630 0.00 0.00 34.41 3.16
4180 4845 9.729281 AAGACCAAGTTTTCTATCCGTAATAAA 57.271 29.630 0.00 0.00 0.00 1.40
4182 4847 8.502105 ACCAAGTTTTCTATCCGTAATAAAGG 57.498 34.615 0.00 0.00 0.00 3.11
4183 4848 7.066645 ACCAAGTTTTCTATCCGTAATAAAGGC 59.933 37.037 0.00 0.00 0.00 4.35
4193 4858 5.318630 TCCGTAATAAAGGCCTGTTCTTTT 58.681 37.500 5.69 0.00 36.12 2.27
4206 4871 5.398012 GCCTGTTCTTTTATCTCCCCACTAT 60.398 44.000 0.00 0.00 0.00 2.12
4234 4899 4.982241 ATTTCTGTCTGTTCCTTCTCCA 57.018 40.909 0.00 0.00 0.00 3.86
4248 4913 4.653341 TCCTTCTCCATCTCTTCATTCTCC 59.347 45.833 0.00 0.00 0.00 3.71
4249 4914 4.408270 CCTTCTCCATCTCTTCATTCTCCA 59.592 45.833 0.00 0.00 0.00 3.86
4257 4922 6.538021 CCATCTCTTCATTCTCCAGTAGTTTG 59.462 42.308 0.00 0.00 0.00 2.93
4278 4943 2.300437 GCTCAGCTATTAATCCCCTCGT 59.700 50.000 0.00 0.00 0.00 4.18
4279 4944 3.862642 GCTCAGCTATTAATCCCCTCGTG 60.863 52.174 0.00 0.00 0.00 4.35
4303 4968 1.135112 TCCACTGTCCATTGTCGATCG 60.135 52.381 9.36 9.36 0.00 3.69
4305 4970 2.481969 CCACTGTCCATTGTCGATCGAT 60.482 50.000 22.50 1.81 0.00 3.59
4307 4972 3.243877 CACTGTCCATTGTCGATCGATTC 59.756 47.826 22.50 10.03 0.00 2.52
4318 4983 1.799181 CGATCGATTCTGAAGCACCGT 60.799 52.381 10.26 0.00 0.00 4.83
4337 5030 2.790433 GTGGCCAAATTCACCTGTAGA 58.210 47.619 7.24 0.00 0.00 2.59
4340 5033 4.947388 GTGGCCAAATTCACCTGTAGATTA 59.053 41.667 7.24 0.00 0.00 1.75
4347 5040 7.229506 CCAAATTCACCTGTAGATTATCCTTCC 59.770 40.741 0.00 0.00 0.00 3.46
4368 5061 0.976641 GTCACTCATCCACTCCACCA 59.023 55.000 0.00 0.00 0.00 4.17
4372 5065 2.816087 CACTCATCCACTCCACCAAAAG 59.184 50.000 0.00 0.00 0.00 2.27
4375 5068 1.270550 CATCCACTCCACCAAAAGCAC 59.729 52.381 0.00 0.00 0.00 4.40
4397 5090 2.027100 ACGAGAAAAGGGGAGATCCAAC 60.027 50.000 0.47 0.00 37.91 3.77
4403 5096 4.637771 GGGAGATCCAACCCAACG 57.362 61.111 13.28 0.00 44.96 4.10
4405 5098 0.392595 GGGAGATCCAACCCAACGAC 60.393 60.000 13.28 0.00 44.96 4.34
4410 5103 0.321298 ATCCAACCCAACGACGAAGG 60.321 55.000 0.00 2.26 0.00 3.46
4411 5104 1.070105 CCAACCCAACGACGAAGGA 59.930 57.895 0.00 0.00 0.00 3.36
4414 5107 0.682852 AACCCAACGACGAAGGATGA 59.317 50.000 0.00 0.00 0.00 2.92
4438 5131 3.432890 GGTCTGATGGATCTCACCTTTCC 60.433 52.174 0.00 0.00 0.00 3.13
4478 5171 1.522580 GGAGAGGGACGCATCAAGC 60.523 63.158 0.00 0.00 40.87 4.01
4531 5224 4.423209 GGCCTCCCTCCTCCCTGT 62.423 72.222 0.00 0.00 0.00 4.00
4532 5225 3.086600 GCCTCCCTCCTCCCTGTG 61.087 72.222 0.00 0.00 0.00 3.66
4533 5226 2.452114 CCTCCCTCCTCCCTGTGT 59.548 66.667 0.00 0.00 0.00 3.72
4534 5227 1.687493 CCTCCCTCCTCCCTGTGTC 60.687 68.421 0.00 0.00 0.00 3.67
4535 5228 2.037367 TCCCTCCTCCCTGTGTCG 59.963 66.667 0.00 0.00 0.00 4.35
4536 5229 3.775654 CCCTCCTCCCTGTGTCGC 61.776 72.222 0.00 0.00 0.00 5.19
4537 5230 3.775654 CCTCCTCCCTGTGTCGCC 61.776 72.222 0.00 0.00 0.00 5.54
4538 5231 2.681778 CTCCTCCCTGTGTCGCCT 60.682 66.667 0.00 0.00 0.00 5.52
4539 5232 2.680352 TCCTCCCTGTGTCGCCTC 60.680 66.667 0.00 0.00 0.00 4.70
4540 5233 3.775654 CCTCCCTGTGTCGCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
4541 5234 3.775654 CTCCCTGTGTCGCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.661563 ATGTAAGATCGTTTGACCACTAAAATA 57.338 29.630 0.00 0.00 0.00 1.40
21 22 7.972832 ATGTAAGATCGTTTGACCACTAAAA 57.027 32.000 0.00 0.00 0.00 1.52
55 57 9.694520 CATCGTTTCACATTAGAAAATACTCTG 57.305 33.333 0.00 0.00 39.05 3.35
72 76 4.301505 GCAGGAGGCATCGTTTCA 57.698 55.556 0.00 0.00 43.97 2.69
217 226 6.767524 TGACTTTTTCTTTAGAAAGCACCA 57.232 33.333 5.20 1.79 43.90 4.17
238 248 2.359850 GGGTGAGCCACGCATTGA 60.360 61.111 14.57 0.00 44.84 2.57
278 288 2.967362 TGAATACGACCCACATGTCAC 58.033 47.619 0.00 0.00 34.88 3.67
359 370 5.584649 TGCAGTAACATAACTTGTCTATGCC 59.415 40.000 0.00 0.00 37.68 4.40
386 397 7.010091 GCTAAAACTTGCAAAATACGGCATTAT 59.990 33.333 0.00 0.00 40.17 1.28
388 399 5.120053 GCTAAAACTTGCAAAATACGGCATT 59.880 36.000 0.00 0.00 40.17 3.56
389 400 4.625311 GCTAAAACTTGCAAAATACGGCAT 59.375 37.500 0.00 0.00 40.17 4.40
390 401 3.984633 GCTAAAACTTGCAAAATACGGCA 59.015 39.130 0.00 0.00 38.46 5.69
391 402 3.984633 TGCTAAAACTTGCAAAATACGGC 59.015 39.130 0.00 2.52 36.15 5.68
392 403 5.219633 AGTGCTAAAACTTGCAAAATACGG 58.780 37.500 0.00 0.00 41.10 4.02
421 432 9.911788 ATAGAACCTGTATCTGATGTTCAATTT 57.088 29.630 16.26 3.73 38.17 1.82
424 435 7.981789 GTCATAGAACCTGTATCTGATGTTCAA 59.018 37.037 16.26 2.37 38.17 2.69
425 436 7.343057 AGTCATAGAACCTGTATCTGATGTTCA 59.657 37.037 16.26 6.60 38.17 3.18
426 437 7.651304 CAGTCATAGAACCTGTATCTGATGTTC 59.349 40.741 9.39 9.39 36.45 3.18
427 438 7.495901 CAGTCATAGAACCTGTATCTGATGTT 58.504 38.462 0.00 0.00 0.00 2.71
428 439 6.462207 GCAGTCATAGAACCTGTATCTGATGT 60.462 42.308 0.00 0.00 0.00 3.06
429 440 5.925397 GCAGTCATAGAACCTGTATCTGATG 59.075 44.000 0.00 0.00 0.00 3.07
430 441 5.011533 GGCAGTCATAGAACCTGTATCTGAT 59.988 44.000 0.00 0.00 0.00 2.90
431 442 4.342378 GGCAGTCATAGAACCTGTATCTGA 59.658 45.833 0.00 0.00 0.00 3.27
432 443 4.100035 TGGCAGTCATAGAACCTGTATCTG 59.900 45.833 0.00 0.00 0.00 2.90
437 448 2.027745 CAGTGGCAGTCATAGAACCTGT 60.028 50.000 0.00 0.00 0.00 4.00
440 451 3.550437 ATCAGTGGCAGTCATAGAACC 57.450 47.619 0.00 0.00 0.00 3.62
473 484 5.172934 ACGGCTTCGAAACTAATGAATACA 58.827 37.500 0.00 0.00 37.63 2.29
502 513 9.295825 AGAAATATATTTGTGTTGTGTCCTTCA 57.704 29.630 15.39 0.00 0.00 3.02
620 664 3.740128 ATCGCATGTGGAGGGTCGC 62.740 63.158 6.39 0.00 0.00 5.19
690 748 0.552848 TTCCATGGGATTGAGGGAGC 59.447 55.000 13.02 0.00 0.00 4.70
919 977 1.333619 GACGAAGCACTTTTTCTGGCA 59.666 47.619 0.00 0.00 0.00 4.92
960 1018 0.674895 ATCTGTTGTTGCCGCTCTCC 60.675 55.000 0.00 0.00 0.00 3.71
1029 1108 7.041030 TGGACTTTGAAAGATAAAATACGTGCA 60.041 33.333 12.53 0.00 0.00 4.57
1138 1360 3.961414 GTGAGGCCGGGGGTCAAA 61.961 66.667 2.18 0.00 0.00 2.69
1372 1837 2.601067 TCCACCTGGTACGCCGAA 60.601 61.111 0.00 0.00 37.67 4.30
1846 2386 2.257676 GAAACTGCTGCAGCTGGC 59.742 61.111 38.20 26.56 43.15 4.85
1865 2407 8.935844 ACTTCCATGAAAAACTCTTTTGAAAAC 58.064 29.630 0.00 0.00 34.83 2.43
1927 2490 1.699634 TCCTTCCCAGTTCACCTTCTG 59.300 52.381 0.00 0.00 0.00 3.02
1928 2491 1.981495 CTCCTTCCCAGTTCACCTTCT 59.019 52.381 0.00 0.00 0.00 2.85
1984 2547 3.494045 GCAATTCCAGTTACCTTGCTC 57.506 47.619 0.00 0.00 39.21 4.26
2014 2578 1.872313 GCTTCTTGCATGCCTAGCTAG 59.128 52.381 16.68 14.20 42.31 3.42
2020 2600 0.327259 TCAGAGCTTCTTGCATGCCT 59.673 50.000 16.68 3.01 45.94 4.75
2021 2601 1.171308 TTCAGAGCTTCTTGCATGCC 58.829 50.000 16.68 0.00 45.94 4.40
2022 2602 3.505464 AATTCAGAGCTTCTTGCATGC 57.495 42.857 11.82 11.82 45.94 4.06
2023 2603 4.599047 GCTAATTCAGAGCTTCTTGCATG 58.401 43.478 0.00 0.00 45.94 4.06
2024 2604 3.311871 CGCTAATTCAGAGCTTCTTGCAT 59.688 43.478 0.00 0.00 45.94 3.96
2025 2605 2.674852 CGCTAATTCAGAGCTTCTTGCA 59.325 45.455 0.00 0.00 45.94 4.08
2026 2606 2.538535 GCGCTAATTCAGAGCTTCTTGC 60.539 50.000 0.00 0.00 45.74 4.01
2027 2607 3.316253 GCGCTAATTCAGAGCTTCTTG 57.684 47.619 0.00 0.00 45.74 3.02
2034 2614 0.179000 ACCCTGGCGCTAATTCAGAG 59.821 55.000 7.64 0.00 0.00 3.35
2035 2615 0.178068 GACCCTGGCGCTAATTCAGA 59.822 55.000 7.64 0.00 0.00 3.27
2038 2618 0.815615 CTGGACCCTGGCGCTAATTC 60.816 60.000 7.64 0.00 0.00 2.17
2046 2626 1.840635 ACTAGAAATCTGGACCCTGGC 59.159 52.381 0.00 0.00 0.00 4.85
2075 2655 5.255397 TGCCTAATCCACCATTATAAGGG 57.745 43.478 14.54 14.54 35.59 3.95
2152 2742 0.748367 GCTTAGCCAGCCAAGGTACC 60.748 60.000 2.73 2.73 43.65 3.34
2203 2801 8.690884 TCAACTTTGAAATGTGGAACTAATCAA 58.309 29.630 0.00 0.00 33.50 2.57
2240 2839 6.976934 AAAAGTTGGGTGTATCAAAGACAT 57.023 33.333 0.00 0.00 0.00 3.06
2547 3155 5.762218 ACTCTTCAAGTGAGAAATGACTTGG 59.238 40.000 11.00 0.00 46.08 3.61
2570 3178 2.033801 GCACTGCCATGGAATATGTGAC 59.966 50.000 18.40 2.84 0.00 3.67
2660 3276 7.234166 ACACAAAATCCAAGAGAATTCCAATCT 59.766 33.333 0.65 0.00 0.00 2.40
2720 3336 2.436292 CCCTCTGTGCTGCAGCTC 60.436 66.667 36.61 32.76 44.66 4.09
2769 3385 2.899303 ATCCTGGGGTAAACTGGTTG 57.101 50.000 0.00 0.00 0.00 3.77
2828 3449 1.202891 AGTTGGTGAAAGTAGGGTGGC 60.203 52.381 0.00 0.00 0.00 5.01
2920 3541 2.604046 GAGCATCGTGAATGGGTAGT 57.396 50.000 0.00 0.00 35.77 2.73
2974 3595 5.398353 CCTTTTACCATCCTGGACTCATCAT 60.398 44.000 0.00 0.00 40.96 2.45
2975 3596 4.080356 CCTTTTACCATCCTGGACTCATCA 60.080 45.833 0.00 0.00 40.96 3.07
2978 3599 3.526899 TCCTTTTACCATCCTGGACTCA 58.473 45.455 0.00 0.00 40.96 3.41
2993 3614 6.256053 ACCAACATAGTCAATGGATCCTTTT 58.744 36.000 14.23 3.93 40.16 2.27
3281 3926 6.209192 ACAATGTTCCATAGAAAATCTGCACA 59.791 34.615 0.00 0.00 27.80 4.57
3327 3973 6.295859 CCAGTAGGAGTTTGCCTGCATATATA 60.296 42.308 0.00 0.00 42.40 0.86
3328 3974 5.513788 CCAGTAGGAGTTTGCCTGCATATAT 60.514 44.000 0.00 0.00 42.40 0.86
3329 3975 4.202357 CCAGTAGGAGTTTGCCTGCATATA 60.202 45.833 0.00 0.00 42.40 0.86
3330 3976 3.434167 CCAGTAGGAGTTTGCCTGCATAT 60.434 47.826 0.00 0.00 42.40 1.78
3420 4066 4.331968 ACCGTTTTCAGCAAGGATCATTA 58.668 39.130 0.00 0.00 0.00 1.90
3459 4107 6.631962 TGTTTAACCGGAAGAAACAATTGTT 58.368 32.000 18.13 18.13 39.46 2.83
3507 4169 8.573035 CATCATAACATTGATCATTCATGTCCA 58.427 33.333 11.06 4.50 34.09 4.02
3533 4196 0.322546 GGTTGGTCCATCCCTGTCAC 60.323 60.000 7.68 0.00 35.97 3.67
3970 4635 3.696548 GGGGAGCAACTTCTTAAGAATGG 59.303 47.826 18.02 10.22 33.01 3.16
3999 4664 3.106827 TGTGCATGGTGAGAGAATAGGA 58.893 45.455 0.00 0.00 0.00 2.94
4006 4671 1.436600 GACAGTGTGCATGGTGAGAG 58.563 55.000 0.00 0.00 0.00 3.20
4045 4710 8.347771 ACATGTTGCATGTCAATATAGAATGAC 58.652 33.333 8.75 0.00 44.84 3.06
4050 4715 7.768120 TGTGTACATGTTGCATGTCAATATAGA 59.232 33.333 16.70 0.00 34.78 1.98
4067 4732 3.786489 GCTGCATCGTTGATGTGTACATG 60.786 47.826 0.00 0.00 41.60 3.21
4080 4745 2.738521 GTGACGTGGCTGCATCGT 60.739 61.111 17.91 17.91 40.49 3.73
4082 4747 1.630244 GAGTGTGACGTGGCTGCATC 61.630 60.000 0.50 0.00 0.00 3.91
4083 4748 1.669115 GAGTGTGACGTGGCTGCAT 60.669 57.895 0.50 0.00 0.00 3.96
4091 4756 1.442769 GGAATGCATGAGTGTGACGT 58.557 50.000 0.00 0.00 0.00 4.34
4093 4758 1.098050 GGGGAATGCATGAGTGTGAC 58.902 55.000 0.00 0.00 0.00 3.67
4094 4759 0.697658 TGGGGAATGCATGAGTGTGA 59.302 50.000 0.00 0.00 0.00 3.58
4097 4762 1.884579 GCTATGGGGAATGCATGAGTG 59.115 52.381 0.00 0.00 0.00 3.51
4109 4774 4.875713 GGTGGGCGTGCTATGGGG 62.876 72.222 0.00 0.00 0.00 4.96
4113 4778 2.365635 AGGAGGTGGGCGTGCTAT 60.366 61.111 0.00 0.00 29.52 2.97
4114 4779 3.075005 GAGGAGGTGGGCGTGCTA 61.075 66.667 0.00 0.00 31.44 3.49
4135 4800 8.072238 TGGTCTTCATTATCGATTAATTCACG 57.928 34.615 1.71 0.00 0.00 4.35
4143 4808 8.567285 AGAAAACTTGGTCTTCATTATCGATT 57.433 30.769 1.71 0.00 0.00 3.34
4146 4811 8.552034 GGATAGAAAACTTGGTCTTCATTATCG 58.448 37.037 0.00 0.00 0.00 2.92
4147 4812 8.552034 CGGATAGAAAACTTGGTCTTCATTATC 58.448 37.037 0.00 0.00 0.00 1.75
4162 4827 6.541278 ACAGGCCTTTATTACGGATAGAAAAC 59.459 38.462 0.00 0.00 0.00 2.43
4163 4828 6.655930 ACAGGCCTTTATTACGGATAGAAAA 58.344 36.000 0.00 0.00 0.00 2.29
4180 4845 2.242452 GGGGAGATAAAAGAACAGGCCT 59.758 50.000 0.00 0.00 0.00 5.19
4182 4847 3.017442 GTGGGGAGATAAAAGAACAGGC 58.983 50.000 0.00 0.00 0.00 4.85
4183 4848 4.576330 AGTGGGGAGATAAAAGAACAGG 57.424 45.455 0.00 0.00 0.00 4.00
4210 4875 7.020827 TGGAGAAGGAACAGACAGAAATAAT 57.979 36.000 0.00 0.00 0.00 1.28
4223 4888 5.988287 AGAATGAAGAGATGGAGAAGGAAC 58.012 41.667 0.00 0.00 0.00 3.62
4227 4892 5.129155 ACTGGAGAATGAAGAGATGGAGAAG 59.871 44.000 0.00 0.00 0.00 2.85
4234 4899 6.070309 AGCAAACTACTGGAGAATGAAGAGAT 60.070 38.462 0.00 0.00 0.00 2.75
4248 4913 6.203723 GGGATTAATAGCTGAGCAAACTACTG 59.796 42.308 7.39 0.00 0.00 2.74
4249 4914 6.292150 GGGATTAATAGCTGAGCAAACTACT 58.708 40.000 7.39 0.00 0.00 2.57
4257 4922 2.300437 ACGAGGGGATTAATAGCTGAGC 59.700 50.000 0.00 0.00 0.00 4.26
4278 4943 2.612721 CGACAATGGACAGTGGATCACA 60.613 50.000 4.72 0.00 36.74 3.58
4279 4944 2.002586 CGACAATGGACAGTGGATCAC 58.997 52.381 4.72 0.00 34.10 3.06
4303 4968 1.648467 GGCCACGGTGCTTCAGAATC 61.648 60.000 1.68 0.00 0.00 2.52
4305 4970 2.281484 GGCCACGGTGCTTCAGAA 60.281 61.111 1.68 0.00 0.00 3.02
4307 4972 1.526575 ATTTGGCCACGGTGCTTCAG 61.527 55.000 3.88 0.00 0.00 3.02
4318 4983 3.737559 ATCTACAGGTGAATTTGGCCA 57.262 42.857 0.00 0.00 0.00 5.36
4337 5030 4.971282 TGGATGAGTGACAGGAAGGATAAT 59.029 41.667 0.00 0.00 0.00 1.28
4340 5033 2.503356 GTGGATGAGTGACAGGAAGGAT 59.497 50.000 0.00 0.00 0.00 3.24
4347 5040 1.066573 GGTGGAGTGGATGAGTGACAG 60.067 57.143 0.00 0.00 0.00 3.51
4368 5061 1.681264 CCCCTTTTCTCGTGTGCTTTT 59.319 47.619 0.00 0.00 0.00 2.27
4372 5065 0.034896 TCTCCCCTTTTCTCGTGTGC 59.965 55.000 0.00 0.00 0.00 4.57
4375 5068 1.555075 TGGATCTCCCCTTTTCTCGTG 59.445 52.381 0.00 0.00 34.29 4.35
4397 5090 1.290203 CATCATCCTTCGTCGTTGGG 58.710 55.000 6.47 1.70 0.00 4.12
4403 5096 3.388308 CATCAGACCATCATCCTTCGTC 58.612 50.000 0.00 0.00 0.00 4.20
4405 5098 2.366590 TCCATCAGACCATCATCCTTCG 59.633 50.000 0.00 0.00 0.00 3.79
4410 5103 4.563168 GGTGAGATCCATCAGACCATCATC 60.563 50.000 0.00 0.00 33.12 2.92
4411 5104 3.327172 GGTGAGATCCATCAGACCATCAT 59.673 47.826 0.00 0.00 33.12 2.45
4414 5107 3.057626 AGGTGAGATCCATCAGACCAT 57.942 47.619 8.84 0.00 34.50 3.55
4438 5131 3.390521 TGCGTCCTACCCAGGCAG 61.391 66.667 0.00 0.00 42.30 4.85
4514 5207 4.423209 ACAGGGAGGAGGGAGGCC 62.423 72.222 0.00 0.00 0.00 5.19
4515 5208 3.086600 CACAGGGAGGAGGGAGGC 61.087 72.222 0.00 0.00 0.00 4.70
4516 5209 1.687493 GACACAGGGAGGAGGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
4517 5210 2.055042 CGACACAGGGAGGAGGGAG 61.055 68.421 0.00 0.00 0.00 4.30
4518 5211 2.037367 CGACACAGGGAGGAGGGA 59.963 66.667 0.00 0.00 0.00 4.20
4519 5212 3.775654 GCGACACAGGGAGGAGGG 61.776 72.222 0.00 0.00 0.00 4.30
4520 5213 3.775654 GGCGACACAGGGAGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
4521 5214 2.681778 AGGCGACACAGGGAGGAG 60.682 66.667 0.00 0.00 0.00 3.69
4522 5215 2.680352 GAGGCGACACAGGGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
4523 5216 3.775654 GGAGGCGACACAGGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
4524 5217 3.775654 GGGAGGCGACACAGGGAG 61.776 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.