Multiple sequence alignment - TraesCS1A01G173100

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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 TraesCS1A01G173100 chr1A 100.000 5181 0 0 1 5181 308817071 308811891 0.000000e+00 9568
1 TraesCS1A01G173100 chr1A 88.944 2026 143 34 2479 4457 37479833 37481824 0.000000e+00 2425
2 TraesCS1A01G173100 chr1A 83.229 638 64 23 1858 2467 37479135 37479757 3.530000e-151 545
3 TraesCS1A01G173100 chr1A 86.145 332 22 10 936 1260 37478494 37478808 2.310000e-88 337
4 TraesCS1A01G173100 chr1A 80.275 436 41 25 216 638 37477932 37478335 2.360000e-73 287
5 TraesCS1A01G173100 chr1A 86.283 226 16 6 1570 1780 37478971 37479196 1.120000e-56 231
6 TraesCS1A01G173100 chr1A 92.857 70 4 1 4529 4597 37481835 37481904 3.300000e-17 100
7 TraesCS1A01G173100 chr1A 93.939 66 2 2 1402 1466 37478860 37478924 1.190000e-16 99
8 TraesCS1A01G173100 chr1B 95.620 2968 93 16 1554 4492 342114960 342117919 0.000000e+00 4726
9 TraesCS1A01G173100 chr1B 90.181 2047 136 24 2479 4475 58323032 58325063 0.000000e+00 2606
10 TraesCS1A01G173100 chr1B 88.242 893 39 22 16 888 342113410 342114256 0.000000e+00 1007
11 TraesCS1A01G173100 chr1B 88.551 690 42 16 4509 5179 342117904 342118575 0.000000e+00 802
12 TraesCS1A01G173100 chr1B 87.034 617 35 22 905 1494 342114241 342114839 0.000000e+00 654
13 TraesCS1A01G173100 chr1B 85.623 626 62 14 1859 2467 58322342 58322956 2.630000e-177 632
14 TraesCS1A01G173100 chr1B 85.326 368 27 18 908 1265 58321677 58322027 6.380000e-94 355
15 TraesCS1A01G173100 chr1B 88.696 115 5 4 735 841 58321554 58321668 3.250000e-27 134
16 TraesCS1A01G173100 chr1B 82.184 174 11 10 1363 1526 58322026 58322189 1.170000e-26 132
17 TraesCS1A01G173100 chr1B 86.290 124 10 2 4581 4697 58325282 58325405 1.510000e-25 128
18 TraesCS1A01G173100 chr1D 93.750 2752 131 19 1793 4513 236804839 236807580 0.000000e+00 4091
19 TraesCS1A01G173100 chr1D 89.742 2057 126 41 2479 4490 38550944 38552960 0.000000e+00 2551
20 TraesCS1A01G173100 chr1D 90.289 762 25 15 122 861 236802438 236803172 0.000000e+00 952
21 TraesCS1A01G173100 chr1D 90.979 654 32 14 4547 5181 236807572 236808217 0.000000e+00 856
22 TraesCS1A01G173100 chr1D 87.342 632 57 12 1858 2467 38550235 38550865 0.000000e+00 702
23 TraesCS1A01G173100 chr1D 83.625 629 39 23 916 1511 236803185 236803782 2.750000e-147 532
24 TraesCS1A01G173100 chr1D 86.040 351 24 15 907 1250 38549640 38549972 2.290000e-93 353
25 TraesCS1A01G173100 chr1D 84.513 226 11 7 1570 1780 38550078 38550294 8.800000e-48 202
26 TraesCS1A01G173100 chr1D 94.366 71 3 1 4529 4598 38552959 38553029 1.970000e-19 108
27 TraesCS1A01G173100 chr7A 85.244 1518 193 18 2655 4168 80853680 80852190 0.000000e+00 1533
28 TraesCS1A01G173100 chr7A 83.784 148 12 6 1107 1244 80854273 80854128 4.210000e-26 130
29 TraesCS1A01G173100 chr7B 84.074 1576 216 20 2655 4221 23442137 23440588 0.000000e+00 1487
30 TraesCS1A01G173100 chr7B 80.676 207 20 12 1051 1244 23442803 23442604 5.410000e-30 143
31 TraesCS1A01G173100 chr7D 83.513 1577 223 22 2655 4221 76733267 76731718 0.000000e+00 1437
32 TraesCS1A01G173100 chr7D 81.188 202 19 11 1051 1239 76733907 76733712 1.500000e-30 145


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 TraesCS1A01G173100 chr1A 308811891 308817071 5180 True 9568.000000 9568 100.000000 1 5181 1 chr1A.!!$R1 5180
1 TraesCS1A01G173100 chr1A 37477932 37481904 3972 False 574.857143 2425 87.381714 216 4597 7 chr1A.!!$F1 4381
2 TraesCS1A01G173100 chr1B 342113410 342118575 5165 False 1797.250000 4726 89.861750 16 5179 4 chr1B.!!$F2 5163
3 TraesCS1A01G173100 chr1B 58321554 58325405 3851 False 664.500000 2606 86.383333 735 4697 6 chr1B.!!$F1 3962
4 TraesCS1A01G173100 chr1D 236802438 236808217 5779 False 1607.750000 4091 89.660750 122 5181 4 chr1D.!!$F2 5059
5 TraesCS1A01G173100 chr1D 38549640 38553029 3389 False 783.200000 2551 88.400600 907 4598 5 chr1D.!!$F1 3691
6 TraesCS1A01G173100 chr7A 80852190 80854273 2083 True 831.500000 1533 84.514000 1107 4168 2 chr7A.!!$R1 3061
7 TraesCS1A01G173100 chr7B 23440588 23442803 2215 True 815.000000 1487 82.375000 1051 4221 2 chr7B.!!$R1 3170
8 TraesCS1A01G173100 chr7D 76731718 76733907 2189 True 791.000000 1437 82.350500 1051 4221 2 chr7D.!!$R1 3170

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
646 684 0.107557 TAGAAAATTCGCCCCGACCC 60.108 55.000 0.00 0.00 34.89 4.46 F
1689 3014 0.109086 CTGATCTTGGAGACACGCGT 60.109 55.000 5.58 5.58 42.67 6.01 F
2965 4470 1.745653 GCCCTGTCCATACTCTTTTGC 59.254 52.381 0.00 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 3183 0.807667 CTGTACATGTCGAGCCCTGC 60.808 60.0 0.00 0.00 0.00 4.85 R
3009 4514 1.009829 CATGGGCGTTAGAGCTTCAC 58.990 55.0 0.00 0.00 37.29 3.18 R
4729 6448 0.739462 GCCAAAATTGTTAGGCGGCC 60.739 55.0 12.11 12.11 37.41 6.13 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
86 87 1.005340 GATCTGCCAGAGACGCTTTG 58.995 55.000 0.00 0.00 31.75 2.77
91 92 1.372087 GCCAGAGACGCTTTGATGGG 61.372 60.000 0.00 0.00 0.00 4.00
110 111 0.461339 GCTCCCATTGGCTGCAATTG 60.461 55.000 0.00 0.00 33.10 2.32
111 112 1.187974 CTCCCATTGGCTGCAATTGA 58.812 50.000 10.34 0.00 0.00 2.57
130 131 2.068519 GATGTCGTGACAACAGCATGA 58.931 47.619 6.80 0.00 45.41 3.07
137 138 3.058708 CGTGACAACAGCATGATCAGTTT 60.059 43.478 0.09 0.00 39.69 2.66
139 140 3.187022 TGACAACAGCATGATCAGTTTCG 59.813 43.478 0.09 0.00 39.69 3.46
205 206 4.450122 CGACACAGCCGCATGCAC 62.450 66.667 19.57 9.19 44.83 4.57
252 253 3.726517 GCGCCGAATATGCCGCAT 61.727 61.111 11.38 11.38 45.21 4.73
253 254 2.174107 CGCCGAATATGCCGCATG 59.826 61.111 16.40 0.00 0.00 4.06
416 423 4.082523 CGCCGTGTCCCCACTGAT 62.083 66.667 0.00 0.00 39.55 2.90
588 626 0.178944 GGCTTAACCCAACCCAACCT 60.179 55.000 0.00 0.00 0.00 3.50
595 633 2.773527 CCAACCCAACCTCCACCCA 61.774 63.158 0.00 0.00 0.00 4.51
599 637 2.115266 CCAACCTCCACCCACACC 59.885 66.667 0.00 0.00 0.00 4.16
600 638 2.281484 CAACCTCCACCCACACCG 60.281 66.667 0.00 0.00 0.00 4.94
601 639 2.446994 AACCTCCACCCACACCGA 60.447 61.111 0.00 0.00 0.00 4.69
602 640 2.073716 AACCTCCACCCACACCGAA 61.074 57.895 0.00 0.00 0.00 4.30
603 641 2.032071 CCTCCACCCACACCGAAC 59.968 66.667 0.00 0.00 0.00 3.95
606 644 3.879885 CCACCCACACCGAACCCA 61.880 66.667 0.00 0.00 0.00 4.51
641 679 2.119671 CGCATTAGAAAATTCGCCCC 57.880 50.000 0.00 0.00 0.00 5.80
642 680 1.596954 CGCATTAGAAAATTCGCCCCG 60.597 52.381 0.00 0.00 0.00 5.73
643 681 1.673920 GCATTAGAAAATTCGCCCCGA 59.326 47.619 0.00 0.00 0.00 5.14
644 682 2.540973 GCATTAGAAAATTCGCCCCGAC 60.541 50.000 0.00 0.00 34.89 4.79
645 683 1.741528 TTAGAAAATTCGCCCCGACC 58.258 50.000 0.00 0.00 34.89 4.79
646 684 0.107557 TAGAAAATTCGCCCCGACCC 60.108 55.000 0.00 0.00 34.89 4.46
647 685 2.361992 AAAATTCGCCCCGACCCC 60.362 61.111 0.00 0.00 34.89 4.95
648 686 4.789123 AAATTCGCCCCGACCCCG 62.789 66.667 0.00 0.00 34.89 5.73
716 754 0.616679 TCCCTCCTTAACCTCCGGTG 60.617 60.000 0.00 0.00 35.34 4.94
750 895 1.219393 CCCTTCTTCCTCGCAGACC 59.781 63.158 0.00 0.00 0.00 3.85
863 1012 1.202417 CGCTCTCTCGTCTCTCTCTCT 60.202 57.143 0.00 0.00 0.00 3.10
864 1013 2.474816 GCTCTCTCGTCTCTCTCTCTC 58.525 57.143 0.00 0.00 0.00 3.20
865 1014 2.803492 GCTCTCTCGTCTCTCTCTCTCC 60.803 59.091 0.00 0.00 0.00 3.71
866 1015 1.407618 TCTCTCGTCTCTCTCTCTCCG 59.592 57.143 0.00 0.00 0.00 4.63
867 1016 0.462375 TCTCGTCTCTCTCTCTCCGG 59.538 60.000 0.00 0.00 0.00 5.14
880 1029 4.888239 TCTCTCTCCGGTTTTACCTATCTG 59.112 45.833 0.00 0.00 35.66 2.90
881 1030 4.607239 TCTCTCCGGTTTTACCTATCTGT 58.393 43.478 0.00 0.00 35.66 3.41
882 1031 5.759059 TCTCTCCGGTTTTACCTATCTGTA 58.241 41.667 0.00 0.00 35.66 2.74
883 1032 6.371278 TCTCTCCGGTTTTACCTATCTGTAT 58.629 40.000 0.00 0.00 35.66 2.29
884 1033 7.520798 TCTCTCCGGTTTTACCTATCTGTATA 58.479 38.462 0.00 0.00 35.66 1.47
885 1034 8.168725 TCTCTCCGGTTTTACCTATCTGTATAT 58.831 37.037 0.00 0.00 35.66 0.86
886 1035 8.345724 TCTCCGGTTTTACCTATCTGTATATC 57.654 38.462 0.00 0.00 35.66 1.63
887 1036 8.168725 TCTCCGGTTTTACCTATCTGTATATCT 58.831 37.037 0.00 0.00 35.66 1.98
888 1037 8.716674 TCCGGTTTTACCTATCTGTATATCTT 57.283 34.615 0.00 0.00 35.66 2.40
889 1038 9.151177 TCCGGTTTTACCTATCTGTATATCTTT 57.849 33.333 0.00 0.00 35.66 2.52
890 1039 9.774413 CCGGTTTTACCTATCTGTATATCTTTT 57.226 33.333 0.00 0.00 35.66 2.27
969 1122 2.273776 GCTGAGGAGGGGGAAAGC 59.726 66.667 0.00 0.00 0.00 3.51
1250 1454 2.313041 CCCTTCCTCCTCCTCCAATTTT 59.687 50.000 0.00 0.00 0.00 1.82
1260 1464 1.181786 CTCCAATTTTGCCGCCCTTA 58.818 50.000 0.00 0.00 0.00 2.69
1270 1474 3.187058 CGCCCTTAATGCGCAGTT 58.813 55.556 18.32 12.77 46.01 3.16
1272 1476 0.109319 CGCCCTTAATGCGCAGTTTT 60.109 50.000 18.32 7.98 46.01 2.43
1273 1477 1.349234 GCCCTTAATGCGCAGTTTTG 58.651 50.000 18.32 6.56 0.00 2.44
1274 1478 1.336795 GCCCTTAATGCGCAGTTTTGT 60.337 47.619 18.32 0.00 0.00 2.83
1275 1479 2.866065 GCCCTTAATGCGCAGTTTTGTT 60.866 45.455 18.32 6.24 0.00 2.83
1277 1481 3.807071 CCCTTAATGCGCAGTTTTGTTTT 59.193 39.130 18.32 4.53 0.00 2.43
1278 1482 4.318689 CCCTTAATGCGCAGTTTTGTTTTG 60.319 41.667 18.32 0.17 0.00 2.44
1317 1613 3.256704 AGGGGATCTCTGTGTGGTTTTA 58.743 45.455 0.00 0.00 0.00 1.52
1318 1614 3.264450 AGGGGATCTCTGTGTGGTTTTAG 59.736 47.826 0.00 0.00 0.00 1.85
1382 1680 2.613223 GGCAGTACTTGGAGAGTTGGAC 60.613 54.545 0.00 0.00 39.86 4.02
1394 1702 4.881850 GGAGAGTTGGACAAGTGAAAAAGA 59.118 41.667 0.00 0.00 0.00 2.52
1465 1780 4.163458 TGTGAGCACATGCAGTATTTTG 57.837 40.909 6.64 0.00 45.16 2.44
1477 1792 4.081752 TGCAGTATTTTGGCAGGTTATTGG 60.082 41.667 0.00 0.00 32.95 3.16
1528 1938 5.862845 CAGCCTATCTGTTCAGGATTACAT 58.137 41.667 0.00 0.00 38.02 2.29
1531 1941 6.784969 AGCCTATCTGTTCAGGATTACATAGT 59.215 38.462 0.00 0.00 33.42 2.12
1533 1943 8.585881 GCCTATCTGTTCAGGATTACATAGTAA 58.414 37.037 0.00 0.00 33.42 2.24
1537 1947 8.824756 TCTGTTCAGGATTACATAGTAAGAGT 57.175 34.615 0.00 0.00 0.00 3.24
1538 1948 9.256228 TCTGTTCAGGATTACATAGTAAGAGTT 57.744 33.333 0.00 0.00 0.00 3.01
1539 1949 9.522804 CTGTTCAGGATTACATAGTAAGAGTTC 57.477 37.037 0.00 0.00 0.00 3.01
1540 1950 8.475639 TGTTCAGGATTACATAGTAAGAGTTCC 58.524 37.037 0.00 0.00 0.00 3.62
1541 1951 7.598759 TCAGGATTACATAGTAAGAGTTCCC 57.401 40.000 0.00 0.00 0.00 3.97
1542 1952 6.264744 TCAGGATTACATAGTAAGAGTTCCCG 59.735 42.308 0.00 0.00 0.00 5.14
1543 1953 5.010820 AGGATTACATAGTAAGAGTTCCCGC 59.989 44.000 0.00 0.00 0.00 6.13
1544 1954 5.221382 GGATTACATAGTAAGAGTTCCCGCA 60.221 44.000 0.00 0.00 0.00 5.69
1545 1955 5.664294 TTACATAGTAAGAGTTCCCGCAA 57.336 39.130 0.00 0.00 0.00 4.85
1546 1956 4.546829 ACATAGTAAGAGTTCCCGCAAA 57.453 40.909 0.00 0.00 0.00 3.68
1547 1957 4.901868 ACATAGTAAGAGTTCCCGCAAAA 58.098 39.130 0.00 0.00 0.00 2.44
1548 1958 5.310451 ACATAGTAAGAGTTCCCGCAAAAA 58.690 37.500 0.00 0.00 0.00 1.94
1588 1998 7.832769 AGTAAGAGACAATTGGACTTAGAGAC 58.167 38.462 10.83 7.08 0.00 3.36
1664 2987 2.413837 GAAAGGCTCGCAAGTTGTAGA 58.586 47.619 4.48 4.06 39.48 2.59
1689 3014 0.109086 CTGATCTTGGAGACACGCGT 60.109 55.000 5.58 5.58 42.67 6.01
1740 3073 5.392125 ACGGTATGGTATAGGAGCTTAACT 58.608 41.667 0.00 0.00 0.00 2.24
1782 3122 3.638627 GCAGCCTAAATAAAGGAGCCAAT 59.361 43.478 0.00 0.00 39.15 3.16
1814 3154 6.564854 AATTAAGCACTACGTATGTTCGTC 57.435 37.500 0.00 0.00 43.12 4.20
1976 3330 6.532988 AGAAGGTAAGAATGGACAGTAGTC 57.467 41.667 0.00 0.00 44.21 2.59
2373 3758 2.007608 GCTTAGGAGGGTGTTTAAGCG 58.992 52.381 0.06 0.00 38.77 4.68
2456 3844 3.319122 ACTTCTTTGTGGAGATTTGTGCC 59.681 43.478 0.00 0.00 0.00 5.01
2475 3863 2.098443 GCCAACGAACTTCTTTTCCACA 59.902 45.455 0.00 0.00 0.00 4.17
2507 3962 5.626142 ACTTCTTTCCTCTTTTCCTTCTCC 58.374 41.667 0.00 0.00 0.00 3.71
2596 4075 7.653647 TGCTAAGAAAACGTTATGGTGATTTT 58.346 30.769 0.00 0.00 0.00 1.82
2612 4095 6.016192 TGGTGATTTTGCCGTCAATTTTAGTA 60.016 34.615 0.00 0.00 31.33 1.82
2932 4430 5.941788 ACTGGATGTCAAAGGTAAGAGTTT 58.058 37.500 0.00 0.00 0.00 2.66
2965 4470 1.745653 GCCCTGTCCATACTCTTTTGC 59.254 52.381 0.00 0.00 0.00 3.68
3009 4514 4.872124 TGCTCAAGTGTGCAGTATTATCAG 59.128 41.667 4.02 0.00 39.29 2.90
3031 4537 0.830648 AAGCTCTAACGCCCATGCTA 59.169 50.000 0.00 0.00 34.43 3.49
3109 4624 0.532640 TGTTGCGTGACAGTGATGCT 60.533 50.000 5.76 0.00 0.00 3.79
3142 4657 0.397957 TTGAGGTATCCGCTGGGCTA 60.398 55.000 0.00 0.00 0.00 3.93
3292 4807 1.079819 CGTCCGCTGTGAGACCAAT 60.080 57.895 0.00 0.00 0.00 3.16
3335 4850 0.040958 CAGTTCGGCTGCAGTTGAAC 60.041 55.000 29.95 29.95 40.69 3.18
3532 5047 3.719268 ATTGAGATTGTGTACAGGCCA 57.281 42.857 5.01 0.00 0.00 5.36
3553 5068 5.664457 CCACTTACAGAGATGTATGAAGCA 58.336 41.667 7.92 0.00 0.00 3.91
3853 5368 0.181350 GGTTCGAAGCATGGAGGGAT 59.819 55.000 21.83 0.00 0.00 3.85
3874 5389 2.637383 GCTGGAGACGGTTCCGACT 61.637 63.158 18.28 16.47 40.27 4.18
4191 5713 1.558756 CCAAAGCTGAGACCAGGAGAT 59.441 52.381 0.00 0.00 40.72 2.75
4295 5834 4.061596 ACTTACTGCTGAGTTCTTCTTGC 58.938 43.478 0.00 0.00 33.21 4.01
4503 6061 8.071122 TGCATTTGTTTTATTCTTGTGTAAGC 57.929 30.769 0.00 0.00 33.82 3.09
4504 6062 7.925483 TGCATTTGTTTTATTCTTGTGTAAGCT 59.075 29.630 0.00 0.00 33.82 3.74
4505 6063 8.764287 GCATTTGTTTTATTCTTGTGTAAGCTT 58.236 29.630 3.48 3.48 33.82 3.74
4507 6065 9.816354 ATTTGTTTTATTCTTGTGTAAGCTTGT 57.184 25.926 9.86 0.00 33.82 3.16
4508 6066 8.627487 TTGTTTTATTCTTGTGTAAGCTTGTG 57.373 30.769 9.86 0.00 33.82 3.33
4509 6067 7.990917 TGTTTTATTCTTGTGTAAGCTTGTGA 58.009 30.769 9.86 0.00 33.82 3.58
4510 6068 8.629158 TGTTTTATTCTTGTGTAAGCTTGTGAT 58.371 29.630 9.86 0.00 33.82 3.06
4511 6069 8.905702 GTTTTATTCTTGTGTAAGCTTGTGATG 58.094 33.333 9.86 0.00 33.82 3.07
4512 6070 4.488126 TTCTTGTGTAAGCTTGTGATGC 57.512 40.909 9.86 0.00 33.82 3.91
4513 6071 3.475575 TCTTGTGTAAGCTTGTGATGCA 58.524 40.909 9.86 0.00 33.82 3.96
4514 6072 4.074259 TCTTGTGTAAGCTTGTGATGCAT 58.926 39.130 9.86 0.00 33.82 3.96
4515 6073 4.154737 TCTTGTGTAAGCTTGTGATGCATC 59.845 41.667 20.14 20.14 33.82 3.91
4516 6074 3.678289 TGTGTAAGCTTGTGATGCATCT 58.322 40.909 26.32 7.85 0.00 2.90
4517 6075 3.686241 TGTGTAAGCTTGTGATGCATCTC 59.314 43.478 26.32 22.77 0.00 2.75
4518 6076 3.937706 GTGTAAGCTTGTGATGCATCTCT 59.062 43.478 26.32 12.71 0.00 3.10
4519 6077 5.111989 GTGTAAGCTTGTGATGCATCTCTA 58.888 41.667 26.32 18.34 0.00 2.43
4520 6078 5.757320 GTGTAAGCTTGTGATGCATCTCTAT 59.243 40.000 26.32 8.72 0.00 1.98
4521 6079 6.925718 GTGTAAGCTTGTGATGCATCTCTATA 59.074 38.462 26.32 11.96 0.00 1.31
4522 6080 7.601886 GTGTAAGCTTGTGATGCATCTCTATAT 59.398 37.037 26.32 12.28 0.00 0.86
4523 6081 7.601508 TGTAAGCTTGTGATGCATCTCTATATG 59.398 37.037 26.32 10.99 0.00 1.78
4524 6082 6.111669 AGCTTGTGATGCATCTCTATATGT 57.888 37.500 26.32 5.84 0.00 2.29
4525 6083 7.237209 AGCTTGTGATGCATCTCTATATGTA 57.763 36.000 26.32 3.65 0.00 2.29
4526 6084 7.095910 AGCTTGTGATGCATCTCTATATGTAC 58.904 38.462 26.32 13.54 0.00 2.90
4527 6085 6.870439 GCTTGTGATGCATCTCTATATGTACA 59.130 38.462 26.32 15.84 0.00 2.90
4534 6101 7.838771 TGCATCTCTATATGTACATTGCATC 57.161 36.000 19.93 2.54 33.09 3.91
4537 6104 7.548427 GCATCTCTATATGTACATTGCATCAGT 59.452 37.037 14.77 0.00 0.00 3.41
4724 6443 5.163754 CCGATTATCTTTCTGTTGGACCAAC 60.164 44.000 27.46 27.46 43.78 3.77
4748 6467 0.739462 GGCCGCCTAACAATTTTGGC 60.739 55.000 0.71 0.36 46.70 4.52
4772 6491 3.749665 TCTTGGAATTTGGCAAGGTTG 57.250 42.857 0.00 0.00 0.00 3.77
4784 6503 1.086696 CAAGGTTGTATGGTGGCGAG 58.913 55.000 0.00 0.00 0.00 5.03
4834 6553 1.918609 GCGACGAAGACATCTTGGTAC 59.081 52.381 9.00 2.35 43.38 3.34
4874 6593 0.034670 AGGTGCATCTCTTCCCTTGC 60.035 55.000 0.00 0.00 35.67 4.01
4969 6708 3.180507 AGCCAGTTCATCTCTCCTTTCT 58.819 45.455 0.00 0.00 0.00 2.52
4970 6709 3.197549 AGCCAGTTCATCTCTCCTTTCTC 59.802 47.826 0.00 0.00 0.00 2.87
5075 6815 0.861837 GGCGTCAAGTGTGAAGACTG 59.138 55.000 0.00 0.00 38.18 3.51
5076 6816 1.538204 GGCGTCAAGTGTGAAGACTGA 60.538 52.381 0.00 0.00 38.18 3.41
5078 6818 2.219674 GCGTCAAGTGTGAAGACTGAAG 59.780 50.000 0.00 0.00 35.47 3.02
5079 6819 3.706698 CGTCAAGTGTGAAGACTGAAGA 58.293 45.455 0.00 0.00 35.47 2.87
5080 6820 3.487574 CGTCAAGTGTGAAGACTGAAGAC 59.512 47.826 0.00 0.00 35.47 3.01
5081 6821 4.688021 GTCAAGTGTGAAGACTGAAGACT 58.312 43.478 0.00 0.00 34.87 3.24
5105 6845 0.319900 ACCTGTCACACATCACGAGC 60.320 55.000 0.00 0.00 0.00 5.03
5131 6871 1.442148 GGAGGAAGATCGGGGTTCG 59.558 63.158 0.00 0.00 40.90 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.643324 GCAGATCCTCTATCCTAAAAGTCTTAA 58.357 37.037 0.00 0.00 34.90 1.85
73 74 1.372087 GCCCATCAAAGCGTCTCTGG 61.372 60.000 0.00 0.00 0.00 3.86
76 77 1.092345 GGAGCCCATCAAAGCGTCTC 61.092 60.000 0.00 0.00 0.00 3.36
91 92 0.461339 CAATTGCAGCCAATGGGAGC 60.461 55.000 0.00 0.00 40.69 4.70
110 111 2.068519 TCATGCTGTTGTCACGACATC 58.931 47.619 0.00 0.00 41.52 3.06
111 112 2.168326 TCATGCTGTTGTCACGACAT 57.832 45.000 0.00 0.00 41.52 3.06
139 140 1.617947 ATTGAGAGCTCCCGGTGACC 61.618 60.000 10.93 0.00 0.00 4.02
275 276 2.102357 CACTCCGTCCATCGTCCG 59.898 66.667 0.00 0.00 37.94 4.79
281 288 2.927856 TGGCCACACTCCGTCCAT 60.928 61.111 0.00 0.00 0.00 3.41
282 289 3.625897 CTGGCCACACTCCGTCCA 61.626 66.667 0.00 0.00 0.00 4.02
416 423 1.682684 GGAGGGCTCCGTTCTCTCA 60.683 63.158 0.00 0.00 40.36 3.27
451 464 2.361104 GCATCCTTTGACGCCCCA 60.361 61.111 0.00 0.00 0.00 4.96
453 466 3.508840 CCGCATCCTTTGACGCCC 61.509 66.667 0.00 0.00 0.00 6.13
470 483 2.281139 GCTCCCCTTATCGCTGCC 60.281 66.667 0.00 0.00 0.00 4.85
588 626 3.562232 GGGTTCGGTGTGGGTGGA 61.562 66.667 0.00 0.00 0.00 4.02
595 633 1.038681 GTTGGGTTTGGGTTCGGTGT 61.039 55.000 0.00 0.00 0.00 4.16
599 637 1.357334 CGTGTTGGGTTTGGGTTCG 59.643 57.895 0.00 0.00 0.00 3.95
600 638 1.066752 GCGTGTTGGGTTTGGGTTC 59.933 57.895 0.00 0.00 0.00 3.62
601 639 2.776913 CGCGTGTTGGGTTTGGGTT 61.777 57.895 0.00 0.00 0.00 4.11
602 640 3.213402 CGCGTGTTGGGTTTGGGT 61.213 61.111 0.00 0.00 0.00 4.51
603 641 4.639171 GCGCGTGTTGGGTTTGGG 62.639 66.667 8.43 0.00 0.00 4.12
719 757 4.357279 AAGGGGTCTGGCAGCTGC 62.357 66.667 30.88 30.88 41.14 5.25
720 758 2.045536 GAAGGGGTCTGGCAGCTG 60.046 66.667 10.11 10.11 0.00 4.24
721 759 1.846712 GAAGAAGGGGTCTGGCAGCT 61.847 60.000 10.34 0.00 36.40 4.24
722 760 1.377856 GAAGAAGGGGTCTGGCAGC 60.378 63.158 10.34 4.94 36.40 5.25
723 761 1.204113 AGGAAGAAGGGGTCTGGCAG 61.204 60.000 8.58 8.58 36.40 4.85
724 762 1.151810 AGGAAGAAGGGGTCTGGCA 60.152 57.895 0.00 0.00 36.40 4.92
725 763 1.604915 GAGGAAGAAGGGGTCTGGC 59.395 63.158 0.00 0.00 36.40 4.85
727 765 1.219393 GCGAGGAAGAAGGGGTCTG 59.781 63.158 0.00 0.00 36.40 3.51
728 766 1.229209 TGCGAGGAAGAAGGGGTCT 60.229 57.895 0.00 0.00 38.69 3.85
863 1012 8.716674 AAGATATACAGATAGGTAAAACCGGA 57.283 34.615 9.46 0.00 44.90 5.14
864 1013 9.774413 AAAAGATATACAGATAGGTAAAACCGG 57.226 33.333 0.00 0.00 44.90 5.28
892 1041 9.847224 GATATACAGATAGGTTTCCCTCAAAAA 57.153 33.333 0.00 0.00 41.45 1.94
893 1042 9.225682 AGATATACAGATAGGTTTCCCTCAAAA 57.774 33.333 0.00 0.00 41.45 2.44
894 1043 8.798975 AGATATACAGATAGGTTTCCCTCAAA 57.201 34.615 0.00 0.00 41.45 2.69
930 1082 1.801512 GCCCACGAACCGTACGTAC 60.802 63.158 15.90 15.90 42.07 3.67
1260 1464 3.181512 CCAACAAAACAAAACTGCGCATT 60.182 39.130 12.24 0.75 0.00 3.56
1267 1471 3.070748 GCACCACCAACAAAACAAAACT 58.929 40.909 0.00 0.00 0.00 2.66
1268 1472 2.159774 CGCACCACCAACAAAACAAAAC 60.160 45.455 0.00 0.00 0.00 2.43
1269 1473 2.069273 CGCACCACCAACAAAACAAAA 58.931 42.857 0.00 0.00 0.00 2.44
1270 1474 1.714794 CGCACCACCAACAAAACAAA 58.285 45.000 0.00 0.00 0.00 2.83
1272 1476 1.153745 GCGCACCACCAACAAAACA 60.154 52.632 0.30 0.00 0.00 2.83
1273 1477 2.227568 CGCGCACCACCAACAAAAC 61.228 57.895 8.75 0.00 0.00 2.43
1274 1478 1.934220 TTCGCGCACCACCAACAAAA 61.934 50.000 8.75 0.00 0.00 2.44
1275 1479 1.729470 ATTCGCGCACCACCAACAAA 61.729 50.000 8.75 0.00 0.00 2.83
1277 1481 0.885150 TAATTCGCGCACCACCAACA 60.885 50.000 8.75 0.00 0.00 3.33
1278 1482 0.179200 CTAATTCGCGCACCACCAAC 60.179 55.000 8.75 0.00 0.00 3.77
1357 1655 0.976641 CTCTCCAAGTACTGCCCACA 59.023 55.000 0.00 0.00 0.00 4.17
1382 1680 5.277828 CCCCTACGTTTCTCTTTTTCACTTG 60.278 44.000 0.00 0.00 0.00 3.16
1386 1684 4.693042 TCCCCTACGTTTCTCTTTTTCA 57.307 40.909 0.00 0.00 0.00 2.69
1394 1702 1.418637 TGCAAGTTCCCCTACGTTTCT 59.581 47.619 0.00 0.00 0.00 2.52
1465 1780 6.534634 AGTAATGATAGACCAATAACCTGCC 58.465 40.000 0.00 0.00 0.00 4.85
1494 1809 4.611310 CAGATAGGCTGTGAACACAATG 57.389 45.455 8.93 0.20 41.33 2.82
1522 1932 5.864418 TGCGGGAACTCTTACTATGTAAT 57.136 39.130 0.00 0.00 0.00 1.89
1552 1962 9.449719 CCAATTGTCTCTTACTATGTTAACCTT 57.550 33.333 4.43 0.00 0.00 3.50
1553 1963 8.822805 TCCAATTGTCTCTTACTATGTTAACCT 58.177 33.333 4.43 0.00 0.00 3.50
1554 1964 8.880750 GTCCAATTGTCTCTTACTATGTTAACC 58.119 37.037 4.43 0.00 0.00 2.85
1555 1965 9.654663 AGTCCAATTGTCTCTTACTATGTTAAC 57.345 33.333 4.43 0.00 0.00 2.01
1558 1968 9.877178 CTAAGTCCAATTGTCTCTTACTATGTT 57.123 33.333 4.43 0.00 0.00 2.71
1559 1969 9.256228 TCTAAGTCCAATTGTCTCTTACTATGT 57.744 33.333 4.43 0.00 0.00 2.29
1560 1970 9.743057 CTCTAAGTCCAATTGTCTCTTACTATG 57.257 37.037 4.43 0.30 0.00 2.23
1561 1971 9.702253 TCTCTAAGTCCAATTGTCTCTTACTAT 57.298 33.333 4.43 0.00 0.00 2.12
1562 1972 8.958506 GTCTCTAAGTCCAATTGTCTCTTACTA 58.041 37.037 4.43 0.31 0.00 1.82
1563 1973 7.672239 AGTCTCTAAGTCCAATTGTCTCTTACT 59.328 37.037 4.43 4.01 0.00 2.24
1564 1974 7.757624 CAGTCTCTAAGTCCAATTGTCTCTTAC 59.242 40.741 4.43 2.08 0.00 2.34
1588 1998 6.428385 GGTTTTCCTCAAGATATCACACAG 57.572 41.667 5.32 0.00 36.94 3.66
1650 2973 3.921021 CAGTTACCTCTACAACTTGCGAG 59.079 47.826 0.00 0.00 32.72 5.03
1664 2987 3.193691 CGTGTCTCCAAGATCAGTTACCT 59.806 47.826 0.00 0.00 0.00 3.08
1689 3014 5.586243 GCTAATGGTCTGCTAATCTGTGAAA 59.414 40.000 0.00 0.00 0.00 2.69
1740 3073 7.040062 AGGCTGCAACACTAATTAACACATTTA 60.040 33.333 0.50 0.00 0.00 1.40
1782 3122 3.866910 CGTAGTGCTTAATTTTAGCCGGA 59.133 43.478 5.05 0.00 37.85 5.14
1795 3135 2.512885 CGACGAACATACGTAGTGCTT 58.487 47.619 0.08 0.00 46.52 3.91
1843 3183 0.807667 CTGTACATGTCGAGCCCTGC 60.808 60.000 0.00 0.00 0.00 4.85
1884 3232 4.035675 CCTTTATTTAGGCTGCAGCACTAC 59.964 45.833 37.63 21.57 44.36 2.73
1890 3238 3.282021 TGCTCCTTTATTTAGGCTGCAG 58.718 45.455 10.11 10.11 38.56 4.41
1976 3330 1.004610 CGATACCTCAAGCATGCAACG 60.005 52.381 21.98 7.60 0.00 4.10
2183 3558 7.148407 CCACAGCTACTTTCACTACATAAAAGG 60.148 40.741 0.00 0.00 34.94 3.11
2185 3560 7.446769 TCCACAGCTACTTTCACTACATAAAA 58.553 34.615 0.00 0.00 0.00 1.52
2373 3758 6.880942 ATCACTCGAGTAGGATAAACTACC 57.119 41.667 19.57 0.00 43.39 3.18
2456 3844 7.486551 TGTTAAATGTGGAAAAGAAGTTCGTTG 59.513 33.333 4.76 0.00 0.00 4.10
2475 3863 9.817809 GGAAAAGAGGAAAGAAGTTTGTTAAAT 57.182 29.630 0.00 0.00 0.00 1.40
2507 3962 2.050714 CCACAGCAAGCAAGCACG 60.051 61.111 3.19 0.00 36.85 5.34
2596 4075 5.172934 AGAACGATACTAAAATTGACGGCA 58.827 37.500 0.00 0.00 0.00 5.69
2932 4430 1.810151 GACAGGGCAAACGAGCATTTA 59.190 47.619 0.00 0.00 35.83 1.40
2965 4470 2.820178 ACCAAAAAGGGATAAGCAGGG 58.180 47.619 0.00 0.00 43.89 4.45
3009 4514 1.009829 CATGGGCGTTAGAGCTTCAC 58.990 55.000 0.00 0.00 37.29 3.18
3109 4624 1.346395 ACCTCAAACAGATGGCGTGTA 59.654 47.619 0.00 0.00 0.00 2.90
3142 4657 4.202409 CCTTCTCCAAGAACCAAAGAGTCT 60.202 45.833 0.00 0.00 29.89 3.24
3335 4850 1.030457 GGAAGCTTCATCATGGCCAG 58.970 55.000 27.02 3.43 0.00 4.85
3532 5047 5.128499 AGCTGCTTCATACATCTCTGTAAGT 59.872 40.000 0.00 0.00 41.09 2.24
3841 5356 1.147824 CAGCGAATCCCTCCATGCT 59.852 57.895 0.00 0.00 0.00 3.79
3853 5368 2.654877 GGAACCGTCTCCAGCGAA 59.345 61.111 0.00 0.00 35.36 4.70
3874 5389 4.171005 CGTACGACCTCAGCTTTTTGATA 58.829 43.478 10.44 0.00 0.00 2.15
4263 5802 2.762887 TCAGCAGTAAGTGGAGGATCAG 59.237 50.000 0.00 0.00 36.25 2.90
4295 5834 1.648720 CCATGGCTAATTCACGGCG 59.351 57.895 4.80 4.80 0.00 6.46
4475 6033 7.337150 ACACAAGAATAAAACAAATGCATCG 57.663 32.000 0.00 0.00 0.00 3.84
4503 6061 8.999220 ATGTACATATAGAGATGCATCACAAG 57.001 34.615 27.81 12.86 0.00 3.16
4504 6062 9.211485 CAATGTACATATAGAGATGCATCACAA 57.789 33.333 27.81 12.76 0.00 3.33
4505 6063 7.332678 GCAATGTACATATAGAGATGCATCACA 59.667 37.037 27.81 18.92 0.00 3.58
4506 6064 7.332678 TGCAATGTACATATAGAGATGCATCAC 59.667 37.037 27.81 21.68 36.46 3.06
4507 6065 7.388437 TGCAATGTACATATAGAGATGCATCA 58.612 34.615 27.81 8.60 36.46 3.07
4508 6066 7.838771 TGCAATGTACATATAGAGATGCATC 57.161 36.000 19.37 19.37 36.46 3.91
4510 6068 7.388437 TGATGCAATGTACATATAGAGATGCA 58.612 34.615 23.87 23.87 44.27 3.96
4511 6069 7.548427 ACTGATGCAATGTACATATAGAGATGC 59.452 37.037 16.08 16.08 0.00 3.91
4512 6070 8.999220 ACTGATGCAATGTACATATAGAGATG 57.001 34.615 9.21 2.91 0.00 2.90
4513 6071 9.650539 GAACTGATGCAATGTACATATAGAGAT 57.349 33.333 9.21 0.00 0.00 2.75
4514 6072 8.090831 GGAACTGATGCAATGTACATATAGAGA 58.909 37.037 9.21 0.00 0.00 3.10
4515 6073 8.093307 AGGAACTGATGCAATGTACATATAGAG 58.907 37.037 9.21 3.73 37.18 2.43
4516 6074 7.966812 AGGAACTGATGCAATGTACATATAGA 58.033 34.615 9.21 0.00 37.18 1.98
4537 6104 4.202233 TGCTCAACATTTCAAATGCAGGAA 60.202 37.500 10.21 0.00 0.00 3.36
4724 6443 0.817013 AATTGTTAGGCGGCCATGTG 59.183 50.000 23.09 0.00 0.00 3.21
4729 6448 0.739462 GCCAAAATTGTTAGGCGGCC 60.739 55.000 12.11 12.11 37.41 6.13
4748 6467 2.610232 CCTTGCCAAATTCCAAGAACGG 60.610 50.000 12.44 0.00 40.59 4.44
4772 6491 1.064060 GATGCAAACTCGCCACCATAC 59.936 52.381 0.00 0.00 0.00 2.39
4784 6503 5.703130 AGAGAACAAGACCTAAGATGCAAAC 59.297 40.000 0.00 0.00 0.00 2.93
4834 6553 3.200483 TCGCTCATCAATCATCACAAGG 58.800 45.455 0.00 0.00 0.00 3.61
4874 6593 2.483745 CAGGCAGCAGCAATCGTG 59.516 61.111 2.65 0.00 44.61 4.35
5075 6815 4.945246 TGTGTGACAGGTTAAGAGTCTTC 58.055 43.478 9.12 0.00 33.56 2.87
5076 6816 5.070446 TGATGTGTGACAGGTTAAGAGTCTT 59.930 40.000 10.87 10.87 33.56 3.01
5078 6818 4.686554 GTGATGTGTGACAGGTTAAGAGTC 59.313 45.833 0.00 0.00 0.00 3.36
5079 6819 4.632153 GTGATGTGTGACAGGTTAAGAGT 58.368 43.478 0.00 0.00 0.00 3.24
5080 6820 3.675225 CGTGATGTGTGACAGGTTAAGAG 59.325 47.826 0.00 0.00 0.00 2.85
5081 6821 3.319689 TCGTGATGTGTGACAGGTTAAGA 59.680 43.478 0.00 0.00 0.00 2.10
5105 6845 1.000283 CCGATCTTCCTCCCTGAATCG 60.000 57.143 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.