Multiple sequence alignment - TraesCS4A01G010700

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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 TraesCS4A01G010700 chr4A 100.000 3075 0 0 1 3075 6020659 6017585 0.000000e+00 5679
1 TraesCS4A01G010700 chr1A 94.161 805 40 4 1 805 323963115 323962318 0.000000e+00 1219
2 TraesCS4A01G010700 chr5A 93.292 805 45 4 1 805 612161205 612160410 0.000000e+00 1179
3 TraesCS4A01G010700 chr5A 94.118 408 21 1 405 812 612160410 612160006 4.360000e-173 617
4 TraesCS4A01G010700 chr5A 91.518 224 16 3 574 797 612160013 612159793 3.850000e-79 305
5 TraesCS4A01G010700 chr5A 80.693 202 31 8 614 811 13418930 13419127 1.910000e-32 150
6 TraesCS4A01G010700 chr4B 92.602 784 41 8 837 1614 579405397 579406169 0.000000e+00 1110
7 TraesCS4A01G010700 chr4B 84.575 953 75 36 1636 2559 579406276 579407185 0.000000e+00 880
8 TraesCS4A01G010700 chr4B 90.869 449 30 7 2631 3075 579407414 579407855 2.640000e-165 592
9 TraesCS4A01G010700 chr4B 80.000 805 108 24 32 805 47656019 47656801 2.080000e-151 545
10 TraesCS4A01G010700 chr4D 91.381 789 56 5 837 1614 463463586 463464373 0.000000e+00 1070
11 TraesCS4A01G010700 chr4D 91.607 417 31 2 2659 3075 463676500 463676912 9.560000e-160 573
12 TraesCS4A01G010700 chr4D 89.417 463 27 7 1636 2089 463464485 463464934 5.760000e-157 564
13 TraesCS4A01G010700 chr4D 89.053 338 25 4 2738 3075 463465673 463465998 2.850000e-110 409
14 TraesCS4A01G010700 chr4D 92.262 168 9 2 2100 2267 463464991 463465154 5.130000e-58 235
15 TraesCS4A01G010700 chr1B 93.792 451 21 4 1 451 342121316 342121759 0.000000e+00 671
16 TraesCS4A01G010700 chr1B 94.721 341 14 2 470 810 342121910 342122246 7.550000e-146 527
17 TraesCS4A01G010700 chr1B 80.317 757 100 23 57 791 613948891 613948162 7.550000e-146 527
18 TraesCS4A01G010700 chr5B 93.541 449 23 3 1 449 692366756 692367198 0.000000e+00 664
19 TraesCS4A01G010700 chr5B 80.574 767 100 23 57 797 470431044 470430301 2.080000e-151 545
20 TraesCS4A01G010700 chr5B 95.122 328 15 1 465 791 692367293 692367620 1.630000e-142 516
21 TraesCS4A01G010700 chr7B 80.050 807 106 27 32 805 583928771 583929555 5.800000e-152 547
22 TraesCS4A01G010700 chr7B 80.063 632 77 26 32 631 583928133 583928747 1.020000e-114 424
23 TraesCS4A01G010700 chr6B 83.333 186 27 4 615 798 216416344 216416161 5.270000e-38 169
24 TraesCS4A01G010700 chr7A 81.915 188 28 6 614 798 483815699 483815883 1.480000e-33 154


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 TraesCS4A01G010700 chr4A 6017585 6020659 3074 True 5679.000000 5679 100.000000 1 3075 1 chr4A.!!$R1 3074
1 TraesCS4A01G010700 chr1A 323962318 323963115 797 True 1219.000000 1219 94.161000 1 805 1 chr1A.!!$R1 804
2 TraesCS4A01G010700 chr5A 612159793 612161205 1412 True 700.333333 1179 92.976000 1 812 3 chr5A.!!$R1 811
3 TraesCS4A01G010700 chr4B 579405397 579407855 2458 False 860.666667 1110 89.348667 837 3075 3 chr4B.!!$F2 2238
4 TraesCS4A01G010700 chr4B 47656019 47656801 782 False 545.000000 545 80.000000 32 805 1 chr4B.!!$F1 773
5 TraesCS4A01G010700 chr4D 463463586 463465998 2412 False 569.500000 1070 90.528250 837 3075 4 chr4D.!!$F2 2238
6 TraesCS4A01G010700 chr1B 342121316 342122246 930 False 599.000000 671 94.256500 1 810 2 chr1B.!!$F1 809
7 TraesCS4A01G010700 chr1B 613948162 613948891 729 True 527.000000 527 80.317000 57 791 1 chr1B.!!$R1 734
8 TraesCS4A01G010700 chr5B 692366756 692367620 864 False 590.000000 664 94.331500 1 791 2 chr5B.!!$F1 790
9 TraesCS4A01G010700 chr5B 470430301 470431044 743 True 545.000000 545 80.574000 57 797 1 chr5B.!!$R1 740
10 TraesCS4A01G010700 chr7B 583928133 583929555 1422 False 485.500000 547 80.056500 32 805 2 chr7B.!!$F1 773

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
909 1996 0.461163 GGCCAAACCGCAAAAGTTGT 60.461 50.0 0.0 0.0 0.0 3.32 F
1624 2758 0.107410 TGCGTCAGAAAACCACCACT 60.107 50.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 3232 0.250081 GGCGGAATCTCCTCATCCAC 60.250 60.0 0.0 0.0 33.3 4.02 R
2947 4436 0.323360 TTGCAGCATAACCCCCTGTC 60.323 55.0 0.0 0.0 0.0 3.51 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
76 77 1.514983 ATCCTGCATGATGGGAGACA 58.485 50.000 3.44 0.00 32.28 3.41
359 364 3.063045 CCTTTGTTCGTATTAAGGCGTCC 59.937 47.826 0.00 0.00 31.59 4.79
391 1048 6.968904 CAGGACGAATATTCAAGATGGTTTTG 59.031 38.462 15.57 3.71 0.00 2.44
392 1049 5.743872 GGACGAATATTCAAGATGGTTTTGC 59.256 40.000 15.57 0.00 0.00 3.68
393 1050 6.404734 GGACGAATATTCAAGATGGTTTTGCT 60.405 38.462 15.57 0.00 0.00 3.91
394 1051 6.924111 ACGAATATTCAAGATGGTTTTGCTT 58.076 32.000 15.57 0.00 0.00 3.91
502 1583 0.614697 TCCACTGATTGCTCCTCCGA 60.615 55.000 0.00 0.00 0.00 4.55
566 1650 4.555348 TTATTCTCGCGGTGTTTGTTTT 57.445 36.364 6.13 0.00 0.00 2.43
724 1811 2.469826 CTGATCGTGCGGCTGTAATTA 58.530 47.619 0.00 0.00 0.00 1.40
755 1842 3.067883 TGTTGTGTGTACGTAAGGCTGTA 59.932 43.478 0.00 0.00 46.39 2.74
870 1957 2.977914 TCTTTTTGAGGATCTCTGGCG 58.022 47.619 0.00 0.00 34.92 5.69
884 1971 1.326245 TCTGGCGAATTTCGTAATGCG 59.674 47.619 19.10 10.53 44.19 4.73
908 1995 1.157257 GGGCCAAACCGCAAAAGTTG 61.157 55.000 4.39 0.00 40.62 3.16
909 1996 0.461163 GGCCAAACCGCAAAAGTTGT 60.461 50.000 0.00 0.00 0.00 3.32
910 1997 1.364721 GCCAAACCGCAAAAGTTGTT 58.635 45.000 0.00 0.00 0.00 2.83
956 2045 1.444553 CCAACCTCTCGTCTCGTGC 60.445 63.158 0.00 0.00 0.00 5.34
975 2064 1.753078 CCCATCCACGTCTCTCCGA 60.753 63.158 0.00 0.00 0.00 4.55
1070 2162 3.827898 GCTCCTGCTCGCCGTACT 61.828 66.667 0.00 0.00 36.03 2.73
1077 2169 4.471726 CTCGCCGTACTCCGCGTT 62.472 66.667 4.92 0.00 37.36 4.84
1269 2361 1.237285 CCAGTGGGGCTTCGTGAAAG 61.237 60.000 0.00 0.00 38.08 2.62
1298 2390 1.468736 GGCGATCTTCCGAACTAACGT 60.469 52.381 0.00 0.00 0.00 3.99
1301 2393 1.844962 GATCTTCCGAACTAACGTCGC 59.155 52.381 0.00 0.00 0.00 5.19
1302 2394 0.453282 TCTTCCGAACTAACGTCGCG 60.453 55.000 0.00 0.00 0.00 5.87
1303 2395 1.995253 CTTCCGAACTAACGTCGCGC 61.995 60.000 0.00 0.00 0.00 6.86
1493 2585 2.278206 CTCGTCATCCGGCTCGTG 60.278 66.667 0.00 0.00 37.11 4.35
1544 2650 2.772691 CGTCTCGCCCCTCAGGTAC 61.773 68.421 0.00 0.00 38.26 3.34
1545 2651 2.439701 TCTCGCCCCTCAGGTACG 60.440 66.667 0.00 0.00 38.26 3.67
1546 2652 4.208686 CTCGCCCCTCAGGTACGC 62.209 72.222 0.00 0.00 38.26 4.42
1573 2679 1.533625 TTGCAAACTCTAAGGCGCAT 58.466 45.000 10.83 0.00 0.00 4.73
1574 2680 1.533625 TGCAAACTCTAAGGCGCATT 58.466 45.000 13.52 13.52 0.00 3.56
1575 2681 2.705730 TGCAAACTCTAAGGCGCATTA 58.294 42.857 14.47 14.47 0.00 1.90
1576 2682 3.278574 TGCAAACTCTAAGGCGCATTAT 58.721 40.909 15.63 0.00 0.00 1.28
1577 2683 3.312421 TGCAAACTCTAAGGCGCATTATC 59.688 43.478 15.63 0.00 0.00 1.75
1578 2684 3.312421 GCAAACTCTAAGGCGCATTATCA 59.688 43.478 15.63 4.29 0.00 2.15
1580 2686 5.683859 CAAACTCTAAGGCGCATTATCATC 58.316 41.667 15.63 0.00 0.00 2.92
1581 2687 3.931578 ACTCTAAGGCGCATTATCATCC 58.068 45.455 15.63 0.00 0.00 3.51
1583 2689 2.637382 TCTAAGGCGCATTATCATCCCA 59.363 45.455 15.63 0.00 0.00 4.37
1584 2690 1.901591 AAGGCGCATTATCATCCCAG 58.098 50.000 5.03 0.00 0.00 4.45
1585 2691 0.607489 AGGCGCATTATCATCCCAGC 60.607 55.000 10.83 0.00 0.00 4.85
1586 2692 0.890542 GGCGCATTATCATCCCAGCA 60.891 55.000 10.83 0.00 0.00 4.41
1598 2704 0.895530 TCCCAGCACAGCAGTAGTAC 59.104 55.000 0.00 0.00 0.00 2.73
1599 2705 0.608130 CCCAGCACAGCAGTAGTACA 59.392 55.000 2.52 0.00 0.00 2.90
1624 2758 0.107410 TGCGTCAGAAAACCACCACT 60.107 50.000 0.00 0.00 0.00 4.00
1625 2759 1.139256 TGCGTCAGAAAACCACCACTA 59.861 47.619 0.00 0.00 0.00 2.74
1626 2760 2.215196 GCGTCAGAAAACCACCACTAA 58.785 47.619 0.00 0.00 0.00 2.24
1666 2870 1.362224 ATTGGTCACTGGCACCTACT 58.638 50.000 0.00 0.00 34.66 2.57
1667 2871 2.018355 TTGGTCACTGGCACCTACTA 57.982 50.000 0.00 0.00 34.66 1.82
1668 2872 1.263356 TGGTCACTGGCACCTACTAC 58.737 55.000 0.00 0.00 34.66 2.73
1695 2899 1.062440 GACGCAATGATCGCAATCACA 59.938 47.619 0.00 0.00 44.51 3.58
1707 2911 8.606040 TGATCGCAATCACAATCATAATCTTA 57.394 30.769 0.00 0.00 36.98 2.10
1708 2912 9.223099 TGATCGCAATCACAATCATAATCTTAT 57.777 29.630 0.00 0.00 36.98 1.73
1709 2913 9.699985 GATCGCAATCACAATCATAATCTTATC 57.300 33.333 0.00 0.00 31.76 1.75
1710 2914 8.837788 TCGCAATCACAATCATAATCTTATCT 57.162 30.769 0.00 0.00 0.00 1.98
1711 2915 9.276590 TCGCAATCACAATCATAATCTTATCTT 57.723 29.630 0.00 0.00 0.00 2.40
1778 2987 1.495584 TTGCTTCACGGAACAGACGC 61.496 55.000 0.00 0.00 34.00 5.19
1789 2998 1.003866 GAACAGACGCACAGTTTGGTC 60.004 52.381 0.00 0.00 43.11 4.02
1814 3023 6.353323 TGGTGACTTTCTGAAGATGTTGTTA 58.647 36.000 0.00 0.00 36.69 2.41
1816 3025 7.173218 TGGTGACTTTCTGAAGATGTTGTTATC 59.827 37.037 0.00 0.00 36.69 1.75
2014 3232 1.672356 CACCGCCAACCAGAGGAAG 60.672 63.158 0.00 0.00 0.00 3.46
2061 3279 2.509916 GCAGGAGGCAGAGGATGG 59.490 66.667 0.00 0.00 43.97 3.51
2078 3296 1.032657 TGGTGCTCCTCGCTAGACTC 61.033 60.000 6.34 0.00 40.11 3.36
2079 3297 1.353804 GTGCTCCTCGCTAGACTCG 59.646 63.158 0.00 0.00 40.11 4.18
2113 3377 3.829948 GAGTGCTCCATCAAAATGTGTG 58.170 45.455 0.00 0.00 0.00 3.82
2114 3378 3.225104 AGTGCTCCATCAAAATGTGTGT 58.775 40.909 0.00 0.00 0.00 3.72
2178 3448 9.778741 TTTTCTTCTTCTGAATGTGTATGTAGT 57.221 29.630 0.00 0.00 0.00 2.73
2201 3471 3.251004 GGAACCAAACTGCTTGACTGTAG 59.749 47.826 0.00 0.00 37.17 2.74
2231 3501 6.391227 TTTTTGGGTCTTTCTGATGAGTTC 57.609 37.500 0.00 0.00 0.00 3.01
2287 3557 5.467035 AAAAACCCATGTTCCACACATAG 57.533 39.130 0.00 0.00 45.06 2.23
2290 3560 2.224992 ACCCATGTTCCACACATAGCAA 60.225 45.455 0.00 0.00 45.06 3.91
2291 3561 2.164219 CCCATGTTCCACACATAGCAAC 59.836 50.000 0.00 0.00 45.06 4.17
2294 3564 4.333649 CCATGTTCCACACATAGCAACTAG 59.666 45.833 0.00 0.00 45.06 2.57
2309 3584 5.598416 GCAACTAGCAAGGGGAAATAAAT 57.402 39.130 0.00 0.00 44.79 1.40
2321 3596 9.313118 CAAGGGGAAATAAATATTAAGCAACAC 57.687 33.333 0.00 0.00 0.00 3.32
2324 3599 9.260002 GGGGAAATAAATATTAAGCAACACATG 57.740 33.333 0.00 0.00 0.00 3.21
2340 3615 3.256631 ACACATGGCTTTTGGCTTCTAAG 59.743 43.478 0.00 0.00 46.20 2.18
2344 3619 3.149196 TGGCTTTTGGCTTCTAAGTCTG 58.851 45.455 0.00 0.00 46.20 3.51
2345 3620 2.095008 GGCTTTTGGCTTCTAAGTCTGC 60.095 50.000 0.00 0.00 42.31 4.26
2374 3649 5.797051 TGGAAGTTAACTACAGCCGTTTAT 58.203 37.500 8.92 0.00 0.00 1.40
2375 3650 5.640357 TGGAAGTTAACTACAGCCGTTTATG 59.360 40.000 8.92 0.00 0.00 1.90
2376 3651 5.446875 GGAAGTTAACTACAGCCGTTTATGC 60.447 44.000 8.92 0.00 0.00 3.14
2377 3652 4.571919 AGTTAACTACAGCCGTTTATGCA 58.428 39.130 6.26 0.00 0.00 3.96
2378 3653 4.390909 AGTTAACTACAGCCGTTTATGCAC 59.609 41.667 6.26 0.00 0.00 4.57
2379 3654 2.465860 ACTACAGCCGTTTATGCACA 57.534 45.000 0.00 0.00 0.00 4.57
2380 3655 2.985896 ACTACAGCCGTTTATGCACAT 58.014 42.857 0.00 0.00 0.00 3.21
2384 3661 4.981806 ACAGCCGTTTATGCACATATTT 57.018 36.364 0.00 0.00 0.00 1.40
2401 3678 8.223100 GCACATATTTGTTTTAAGAAGCAAAGG 58.777 33.333 7.13 3.24 45.12 3.11
2403 3680 5.905480 ATTTGTTTTAAGAAGCAAAGGCG 57.095 34.783 7.13 0.00 45.12 5.52
2404 3681 5.356426 ATTTGTTTTAAGAAGCAAAGGCGT 58.644 33.333 7.13 0.00 45.12 5.68
2407 3684 7.683463 ATTTGTTTTAAGAAGCAAAGGCGTACT 60.683 33.333 7.13 0.00 45.12 2.73
2419 3696 5.223382 CAAAGGCGTACTGGATATCTGTAG 58.777 45.833 2.05 2.11 31.79 2.74
2420 3697 3.422796 AGGCGTACTGGATATCTGTAGG 58.577 50.000 16.91 16.91 38.13 3.18
2422 3699 2.094649 GCGTACTGGATATCTGTAGGGC 60.095 54.545 19.89 16.00 36.68 5.19
2423 3700 3.422796 CGTACTGGATATCTGTAGGGCT 58.577 50.000 2.05 0.00 34.32 5.19
2428 3705 3.165875 TGGATATCTGTAGGGCTAGCAC 58.834 50.000 18.24 14.32 0.00 4.40
2438 3715 5.333581 TGTAGGGCTAGCACATAGTATGAT 58.666 41.667 21.39 0.00 33.65 2.45
2439 3716 4.815533 AGGGCTAGCACATAGTATGATG 57.184 45.455 21.39 11.63 33.65 3.07
2440 3717 4.163427 AGGGCTAGCACATAGTATGATGT 58.837 43.478 21.39 3.11 40.78 3.06
2441 3718 5.333581 AGGGCTAGCACATAGTATGATGTA 58.666 41.667 21.39 4.05 37.99 2.29
2442 3719 5.960811 AGGGCTAGCACATAGTATGATGTAT 59.039 40.000 21.39 7.25 37.99 2.29
2443 3720 6.045318 GGGCTAGCACATAGTATGATGTATG 58.955 44.000 18.24 5.35 37.99 2.39
2444 3721 5.521735 GGCTAGCACATAGTATGATGTATGC 59.478 44.000 18.24 14.46 37.99 3.14
2462 3755 9.962759 GATGTATGCTCAATGAAAAATGTTTTC 57.037 29.630 6.53 6.53 0.00 2.29
2469 3762 9.853921 GCTCAATGAAAAATGTTTTCTAAACAG 57.146 29.630 13.09 5.74 33.18 3.16
2477 3770 9.883142 AAAAATGTTTTCTAAACAGATCCACAA 57.117 25.926 10.34 0.00 33.18 3.33
2480 3773 9.883142 AATGTTTTCTAAACAGATCCACAAAAA 57.117 25.926 10.34 0.00 33.18 1.94
2486 3779 9.959749 TTCTAAACAGATCCACAAAAATTACAC 57.040 29.630 0.00 0.00 0.00 2.90
2497 3790 5.454232 CACAAAAATTACACGACAAGGTCAC 59.546 40.000 0.00 0.00 32.09 3.67
2500 3793 3.746045 ATTACACGACAAGGTCACAGT 57.254 42.857 0.00 0.00 32.09 3.55
2503 3796 3.530265 ACACGACAAGGTCACAGTTTA 57.470 42.857 0.00 0.00 32.09 2.01
2506 3799 3.736252 CACGACAAGGTCACAGTTTAGAG 59.264 47.826 0.00 0.00 32.09 2.43
2520 3813 4.020662 CAGTTTAGAGGGTTCTTCTCTGCT 60.021 45.833 4.10 0.00 41.25 4.24
2531 3824 5.279056 GGTTCTTCTCTGCTACTGTACTTGT 60.279 44.000 0.00 0.00 0.00 3.16
2532 3825 6.217294 GTTCTTCTCTGCTACTGTACTTGTT 58.783 40.000 0.00 0.00 0.00 2.83
2533 3826 7.368833 GTTCTTCTCTGCTACTGTACTTGTTA 58.631 38.462 0.00 0.00 0.00 2.41
2540 3833 6.152154 TCTGCTACTGTACTTGTTATACTGCA 59.848 38.462 0.00 0.00 0.00 4.41
2560 3853 1.883678 TCCTGAATGGATCCAGCAGA 58.116 50.000 33.10 22.11 40.56 4.26
2561 3854 1.767088 TCCTGAATGGATCCAGCAGAG 59.233 52.381 33.10 25.62 40.56 3.35
2565 3858 2.169978 TGAATGGATCCAGCAGAGACAG 59.830 50.000 21.33 0.00 0.00 3.51
2569 3862 2.324541 GGATCCAGCAGAGACAGGTAT 58.675 52.381 6.95 0.00 0.00 2.73
2586 3879 2.289002 GGTATCTGCAAGCATTCTTCCG 59.711 50.000 0.00 0.00 0.00 4.30
2601 3912 1.852157 TTCCGGCTCAAGGGCTGAAT 61.852 55.000 1.45 0.00 38.39 2.57
2611 3922 6.467677 GCTCAAGGGCTGAATCATATACTAA 58.532 40.000 0.00 0.00 32.17 2.24
2640 4129 7.658261 ACAACATACTATAGTGTACGATGCAT 58.342 34.615 15.90 0.00 0.00 3.96
2671 4160 6.040842 ACATTACTGAACAACTTGGAGCATTT 59.959 34.615 0.00 0.00 0.00 2.32
2682 4171 8.752187 ACAACTTGGAGCATTTTCATATGTATT 58.248 29.630 1.90 0.00 0.00 1.89
2696 4185 6.207928 TCATATGTATTGCAAAATTCCTGCG 58.792 36.000 1.71 0.00 42.97 5.18
2711 4200 1.613255 CCTGCGAACTTTGTATGGGGT 60.613 52.381 0.00 0.00 0.00 4.95
2712 4201 1.737793 CTGCGAACTTTGTATGGGGTC 59.262 52.381 0.00 0.00 0.00 4.46
2811 4300 1.202940 GGGGACTTTTGAGAGGCAAGT 60.203 52.381 0.00 0.00 37.87 3.16
2907 4396 1.909302 TCCAACCTCACATTCTCTCCC 59.091 52.381 0.00 0.00 0.00 4.30
2925 4414 0.523072 CCAAGCACCTGAAACCATCG 59.477 55.000 0.00 0.00 0.00 3.84
2926 4415 0.523072 CAAGCACCTGAAACCATCGG 59.477 55.000 0.00 0.00 0.00 4.18
2938 4427 0.108138 ACCATCGGAAGCACACTAGC 60.108 55.000 0.00 0.00 0.00 3.42
2939 4428 0.108186 CCATCGGAAGCACACTAGCA 60.108 55.000 0.00 0.00 36.85 3.49
2940 4429 1.284657 CATCGGAAGCACACTAGCAG 58.715 55.000 0.00 0.00 36.85 4.24
2944 4433 2.094700 TCGGAAGCACACTAGCAGTAAG 60.095 50.000 0.00 0.00 36.85 2.34
2970 4459 2.236893 CAGGGGGTTATGCTGCAATTTT 59.763 45.455 6.36 0.00 0.00 1.82
2971 4460 2.501316 AGGGGGTTATGCTGCAATTTTC 59.499 45.455 6.36 0.00 0.00 2.29
2982 4471 5.833082 TGCTGCAATTTTCAAATTTGCATT 58.167 29.167 25.19 8.44 39.38 3.56
2990 4483 9.160576 CAATTTTCAAATTTGCATTACAGTGTG 57.839 29.630 13.54 0.00 36.52 3.82
3001 4494 5.010516 TGCATTACAGTGTGGCAATTTTACT 59.989 36.000 14.28 0.00 0.00 2.24
3002 4495 6.207614 TGCATTACAGTGTGGCAATTTTACTA 59.792 34.615 14.28 0.00 0.00 1.82
3003 4496 6.747280 GCATTACAGTGTGGCAATTTTACTAG 59.253 38.462 5.88 0.00 0.00 2.57
3004 4497 7.574967 GCATTACAGTGTGGCAATTTTACTAGT 60.575 37.037 5.88 0.00 0.00 2.57
3005 4498 8.941977 CATTACAGTGTGGCAATTTTACTAGTA 58.058 33.333 5.88 0.00 0.00 1.82
3006 4499 9.681062 ATTACAGTGTGGCAATTTTACTAGTAT 57.319 29.630 5.88 0.00 0.00 2.12
3007 4500 7.996098 ACAGTGTGGCAATTTTACTAGTATT 57.004 32.000 2.79 0.00 0.00 1.89
3008 4501 8.404107 ACAGTGTGGCAATTTTACTAGTATTT 57.596 30.769 2.79 0.00 0.00 1.40
3050 4543 4.458989 TGGTAAGCAATGGAGCAAAAGTAG 59.541 41.667 0.00 0.00 36.85 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.318784 GGATTAGTTCCGATCGCGCT 60.319 55.000 10.32 9.37 33.93 5.92
97 101 1.519719 GTGCGATGCCTTCTCCTCT 59.480 57.895 0.00 0.00 0.00 3.69
312 317 2.383527 CCAGCGGCTCTTCACGTTC 61.384 63.158 0.00 0.00 0.00 3.95
359 364 7.482654 TCTTGAATATTCGTCCTGCAAATAG 57.517 36.000 10.80 0.00 0.00 1.73
435 1093 3.550639 CGCATGCACCAGGTAATTATTGG 60.551 47.826 19.57 14.24 37.98 3.16
502 1583 9.247861 AGAGAAAGAAAATAACTACCATGCATT 57.752 29.630 0.00 0.00 0.00 3.56
566 1650 6.205464 CCCGTTCGTGTATCCTATAAACTAGA 59.795 42.308 0.00 0.00 0.00 2.43
724 1811 2.346244 CGTACACACAACAACACGAACT 59.654 45.455 0.00 0.00 0.00 3.01
755 1842 6.432936 CAAACATATTCATCGCTAAGTGCAT 58.567 36.000 0.00 0.00 43.06 3.96
834 1921 9.929180 CCTCAAAAAGATACGGATATTCATCTA 57.071 33.333 0.00 0.00 0.00 1.98
835 1922 8.651389 TCCTCAAAAAGATACGGATATTCATCT 58.349 33.333 0.00 0.00 0.00 2.90
884 1971 2.022240 TTTGCGGTTTGGCCCTTGTC 62.022 55.000 0.00 0.00 0.00 3.18
956 2045 2.786495 CGGAGAGACGTGGATGGGG 61.786 68.421 0.00 0.00 0.00 4.96
975 2064 4.681978 GAGTTGGAGCGGGCACGT 62.682 66.667 11.45 0.00 43.45 4.49
1053 2145 3.759766 GAGTACGGCGAGCAGGAGC 62.760 68.421 16.62 0.00 42.56 4.70
1251 2343 2.247790 CTTTCACGAAGCCCCACTG 58.752 57.895 0.00 0.00 0.00 3.66
1277 2369 1.568606 GTTAGTTCGGAAGATCGCCC 58.431 55.000 0.00 0.00 41.60 6.13
1329 2421 2.750657 CCACCATCCTCTGCCTCCC 61.751 68.421 0.00 0.00 0.00 4.30
1523 2615 2.725008 CTGAGGGGCGAGACGATC 59.275 66.667 0.00 0.00 0.00 3.69
1548 2654 3.568538 GCCTTAGAGTTTGCAATGTGTG 58.431 45.455 0.00 0.00 0.00 3.82
1549 2655 2.226437 CGCCTTAGAGTTTGCAATGTGT 59.774 45.455 0.00 0.00 0.00 3.72
1563 2669 3.005554 CTGGGATGATAATGCGCCTTAG 58.994 50.000 4.18 0.00 0.00 2.18
1568 2674 0.239347 GTGCTGGGATGATAATGCGC 59.761 55.000 0.00 0.00 0.00 6.09
1573 2679 1.561076 ACTGCTGTGCTGGGATGATAA 59.439 47.619 0.00 0.00 0.00 1.75
1574 2680 1.206878 ACTGCTGTGCTGGGATGATA 58.793 50.000 0.00 0.00 0.00 2.15
1575 2681 1.140452 CTACTGCTGTGCTGGGATGAT 59.860 52.381 6.48 0.00 0.00 2.45
1576 2682 0.538584 CTACTGCTGTGCTGGGATGA 59.461 55.000 6.48 0.00 0.00 2.92
1577 2683 0.251354 ACTACTGCTGTGCTGGGATG 59.749 55.000 6.48 0.00 0.00 3.51
1578 2684 1.482593 GTACTACTGCTGTGCTGGGAT 59.517 52.381 6.48 0.00 0.00 3.85
1580 2686 0.608130 TGTACTACTGCTGTGCTGGG 59.392 55.000 6.48 0.00 0.00 4.45
1581 2687 2.455674 TTGTACTACTGCTGTGCTGG 57.544 50.000 6.48 0.00 0.00 4.85
1583 2689 4.271696 TCATTTGTACTACTGCTGTGCT 57.728 40.909 6.48 0.00 0.00 4.40
1584 2690 4.728882 GCATCATTTGTACTACTGCTGTGC 60.729 45.833 6.48 0.09 0.00 4.57
1585 2691 4.493057 CGCATCATTTGTACTACTGCTGTG 60.493 45.833 6.48 0.00 0.00 3.66
1586 2692 3.618594 CGCATCATTTGTACTACTGCTGT 59.381 43.478 0.66 0.66 0.00 4.40
1598 2704 3.670055 GTGGTTTTCTGACGCATCATTTG 59.330 43.478 0.00 0.00 33.22 2.32
1599 2705 3.305335 GGTGGTTTTCTGACGCATCATTT 60.305 43.478 0.00 0.00 33.22 2.32
1625 2759 8.521176 CCAATTTCAAGTTCTCTGAATCATCTT 58.479 33.333 0.00 0.00 0.00 2.40
1626 2760 7.668886 ACCAATTTCAAGTTCTCTGAATCATCT 59.331 33.333 0.00 0.00 0.00 2.90
1666 2870 3.702330 CGATCATTGCGTCTTAGTGGTA 58.298 45.455 0.00 0.00 0.00 3.25
1667 2871 2.540515 CGATCATTGCGTCTTAGTGGT 58.459 47.619 0.00 0.00 0.00 4.16
1668 2872 1.258982 GCGATCATTGCGTCTTAGTGG 59.741 52.381 0.00 0.00 0.00 4.00
1707 2911 7.040494 GCCTCCTTACGACTTTTAACTAAGAT 58.960 38.462 0.00 0.00 0.00 2.40
1708 2912 6.393171 GCCTCCTTACGACTTTTAACTAAGA 58.607 40.000 0.00 0.00 0.00 2.10
1709 2913 5.287992 CGCCTCCTTACGACTTTTAACTAAG 59.712 44.000 0.00 0.00 0.00 2.18
1710 2914 5.163513 CGCCTCCTTACGACTTTTAACTAA 58.836 41.667 0.00 0.00 0.00 2.24
1711 2915 4.737054 CGCCTCCTTACGACTTTTAACTA 58.263 43.478 0.00 0.00 0.00 2.24
1712 2916 3.582780 CGCCTCCTTACGACTTTTAACT 58.417 45.455 0.00 0.00 0.00 2.24
1778 2987 2.332063 AGTCACCAGACCAAACTGTG 57.668 50.000 0.00 0.00 46.15 3.66
1789 2998 4.818546 ACAACATCTTCAGAAAGTCACCAG 59.181 41.667 0.00 0.00 33.95 4.00
1837 3046 1.475280 CGGAAGATGTTCAGGTACGGA 59.525 52.381 4.83 0.00 33.93 4.69
1983 3201 4.803426 CGGTGAGCTCGTCAGGGC 62.803 72.222 9.64 0.00 46.47 5.19
2014 3232 0.250081 GGCGGAATCTCCTCATCCAC 60.250 60.000 0.00 0.00 33.30 4.02
2103 3362 3.182173 GCCGAATGACAACACACATTTTG 59.818 43.478 0.00 0.00 36.94 2.44
2113 3377 1.075542 TCGACATGCCGAATGACAAC 58.924 50.000 0.10 0.00 38.72 3.32
2114 3378 1.802069 TTCGACATGCCGAATGACAA 58.198 45.000 13.10 0.00 42.74 3.18
2178 3448 2.023673 CAGTCAAGCAGTTTGGTTCCA 58.976 47.619 0.00 0.00 35.69 3.53
2231 3501 4.046462 CACAAGCAATCAACAAAGTGAGG 58.954 43.478 0.00 0.00 0.00 3.86
2273 3543 4.565444 TGCTAGTTGCTATGTGTGGAACAT 60.565 41.667 0.00 0.00 46.73 2.71
2274 3544 3.244387 TGCTAGTTGCTATGTGTGGAACA 60.244 43.478 0.00 0.00 44.26 3.18
2275 3545 3.334691 TGCTAGTTGCTATGTGTGGAAC 58.665 45.455 0.00 0.00 43.37 3.62
2279 3549 2.679837 CCCTTGCTAGTTGCTATGTGTG 59.320 50.000 0.00 0.00 43.37 3.82
2281 3551 2.092968 TCCCCTTGCTAGTTGCTATGTG 60.093 50.000 0.00 0.00 43.37 3.21
2282 3552 2.196595 TCCCCTTGCTAGTTGCTATGT 58.803 47.619 0.00 0.00 43.37 2.29
2283 3553 3.281727 TTCCCCTTGCTAGTTGCTATG 57.718 47.619 0.00 0.00 43.37 2.23
2285 3555 5.444744 TTATTTCCCCTTGCTAGTTGCTA 57.555 39.130 0.00 0.00 43.37 3.49
2286 3556 2.907458 ATTTCCCCTTGCTAGTTGCT 57.093 45.000 0.00 0.00 43.37 3.91
2287 3557 5.598416 ATTTATTTCCCCTTGCTAGTTGC 57.402 39.130 0.00 0.00 43.25 4.17
2290 3560 9.078990 GCTTAATATTTATTTCCCCTTGCTAGT 57.921 33.333 0.00 0.00 0.00 2.57
2291 3561 9.077885 TGCTTAATATTTATTTCCCCTTGCTAG 57.922 33.333 0.00 0.00 0.00 3.42
2294 3564 7.984617 TGTTGCTTAATATTTATTTCCCCTTGC 59.015 33.333 0.00 0.00 0.00 4.01
2301 3571 9.533253 AGCCATGTGTTGCTTAATATTTATTTC 57.467 29.630 0.00 0.00 32.94 2.17
2309 3584 5.477510 CCAAAAGCCATGTGTTGCTTAATA 58.522 37.500 7.26 0.00 46.58 0.98
2321 3596 3.760684 AGACTTAGAAGCCAAAAGCCATG 59.239 43.478 0.00 0.00 45.47 3.66
2324 3599 2.095008 GCAGACTTAGAAGCCAAAAGCC 60.095 50.000 0.00 0.00 45.47 4.35
2330 3605 0.532573 CCTCGCAGACTTAGAAGCCA 59.467 55.000 0.00 0.00 0.00 4.75
2340 3615 2.930682 GTTAACTTCCATCCTCGCAGAC 59.069 50.000 0.00 0.00 0.00 3.51
2344 3619 4.113354 CTGTAGTTAACTTCCATCCTCGC 58.887 47.826 14.49 0.00 0.00 5.03
2345 3620 4.113354 GCTGTAGTTAACTTCCATCCTCG 58.887 47.826 14.49 0.98 0.00 4.63
2374 3649 8.654230 TTTGCTTCTTAAAACAAATATGTGCA 57.346 26.923 0.00 0.00 40.46 4.57
2375 3650 8.223100 CCTTTGCTTCTTAAAACAAATATGTGC 58.777 33.333 0.00 0.00 40.46 4.57
2376 3651 8.223100 GCCTTTGCTTCTTAAAACAAATATGTG 58.777 33.333 0.00 0.00 35.48 3.21
2377 3652 7.116233 CGCCTTTGCTTCTTAAAACAAATATGT 59.884 33.333 0.00 0.00 36.94 2.29
2378 3653 7.116233 ACGCCTTTGCTTCTTAAAACAAATATG 59.884 33.333 0.00 0.00 31.85 1.78
2379 3654 7.151976 ACGCCTTTGCTTCTTAAAACAAATAT 58.848 30.769 0.00 0.00 31.85 1.28
2380 3655 6.508777 ACGCCTTTGCTTCTTAAAACAAATA 58.491 32.000 0.00 0.00 31.85 1.40
2384 3661 4.577283 AGTACGCCTTTGCTTCTTAAAACA 59.423 37.500 0.00 0.00 34.43 2.83
2401 3678 2.094649 GCCCTACAGATATCCAGTACGC 60.095 54.545 0.00 2.63 0.00 4.42
2403 3680 4.399934 GCTAGCCCTACAGATATCCAGTAC 59.600 50.000 2.29 0.00 0.00 2.73
2404 3681 4.044191 TGCTAGCCCTACAGATATCCAGTA 59.956 45.833 13.29 2.50 0.00 2.74
2407 3684 3.165875 GTGCTAGCCCTACAGATATCCA 58.834 50.000 13.29 0.00 0.00 3.41
2409 3686 5.654650 ACTATGTGCTAGCCCTACAGATATC 59.345 44.000 13.29 0.00 0.00 1.63
2411 3688 4.999310 ACTATGTGCTAGCCCTACAGATA 58.001 43.478 13.29 0.54 0.00 1.98
2419 3696 4.543590 ACATCATACTATGTGCTAGCCC 57.456 45.455 13.29 0.00 38.65 5.19
2420 3697 5.521735 GCATACATCATACTATGTGCTAGCC 59.478 44.000 13.29 4.15 40.29 3.93
2422 3699 7.542025 TGAGCATACATCATACTATGTGCTAG 58.458 38.462 9.82 0.00 38.56 3.42
2423 3700 7.466746 TGAGCATACATCATACTATGTGCTA 57.533 36.000 9.82 0.53 38.56 3.49
2442 3719 9.376075 TGTTTAGAAAACATTTTTCATTGAGCA 57.624 25.926 12.63 2.98 0.00 4.26
2443 3720 9.853921 CTGTTTAGAAAACATTTTTCATTGAGC 57.146 29.630 12.63 0.99 0.00 4.26
2456 3749 9.883142 AATTTTTGTGGATCTGTTTAGAAAACA 57.117 25.926 5.22 5.22 36.32 2.83
2462 3755 8.286800 TCGTGTAATTTTTGTGGATCTGTTTAG 58.713 33.333 0.00 0.00 0.00 1.85
2467 3760 5.996219 TGTCGTGTAATTTTTGTGGATCTG 58.004 37.500 0.00 0.00 0.00 2.90
2469 3762 5.856455 CCTTGTCGTGTAATTTTTGTGGATC 59.144 40.000 0.00 0.00 0.00 3.36
2477 3770 4.879545 ACTGTGACCTTGTCGTGTAATTTT 59.120 37.500 0.00 0.00 34.95 1.82
2480 3773 3.746045 ACTGTGACCTTGTCGTGTAAT 57.254 42.857 0.00 0.00 34.95 1.89
2486 3779 3.318017 CCTCTAAACTGTGACCTTGTCG 58.682 50.000 0.00 0.00 34.95 4.35
2497 3790 4.020662 AGCAGAGAAGAACCCTCTAAACTG 60.021 45.833 0.00 0.00 38.84 3.16
2500 3793 5.186021 CAGTAGCAGAGAAGAACCCTCTAAA 59.814 44.000 0.00 0.00 38.84 1.85
2503 3796 3.096092 CAGTAGCAGAGAAGAACCCTCT 58.904 50.000 0.00 0.00 41.35 3.69
2506 3799 3.764972 AGTACAGTAGCAGAGAAGAACCC 59.235 47.826 0.00 0.00 0.00 4.11
2520 3813 7.340999 TCAGGATGCAGTATAACAAGTACAGTA 59.659 37.037 0.00 0.00 34.76 2.74
2557 3850 2.093816 TGCTTGCAGATACCTGTCTCTG 60.094 50.000 7.99 7.99 42.35 3.35
2558 3851 2.182827 TGCTTGCAGATACCTGTCTCT 58.817 47.619 0.00 0.00 42.35 3.10
2559 3852 2.680312 TGCTTGCAGATACCTGTCTC 57.320 50.000 0.00 0.00 42.35 3.36
2560 3853 3.199508 AGAATGCTTGCAGATACCTGTCT 59.800 43.478 0.87 0.00 42.35 3.41
2561 3854 3.539604 AGAATGCTTGCAGATACCTGTC 58.460 45.455 0.87 0.00 42.35 3.51
2565 3858 2.289002 CGGAAGAATGCTTGCAGATACC 59.711 50.000 5.71 0.00 41.99 2.73
2569 3862 1.308069 GCCGGAAGAATGCTTGCAGA 61.308 55.000 5.05 0.00 41.99 4.26
2586 3879 2.645838 TATGATTCAGCCCTTGAGCC 57.354 50.000 0.00 0.00 37.07 4.70
2640 4129 6.544197 TCCAAGTTGTTCAGTAATGTTGCTAA 59.456 34.615 1.45 0.00 0.00 3.09
2671 4160 6.696583 CGCAGGAATTTTGCAATACATATGAA 59.303 34.615 10.38 0.00 41.59 2.57
2682 4171 3.122297 CAAAGTTCGCAGGAATTTTGCA 58.878 40.909 13.97 0.00 46.10 4.08
2696 4185 5.476945 ACTTGAATGACCCCATACAAAGTTC 59.523 40.000 0.00 0.00 31.43 3.01
2711 4200 4.698780 CAGAGCATTCCTGAACTTGAATGA 59.301 41.667 14.51 0.00 46.89 2.57
2712 4201 4.458295 ACAGAGCATTCCTGAACTTGAATG 59.542 41.667 7.65 7.65 46.74 2.67
2811 4300 2.486982 CGAGGTCGTCTTGGACTTCTTA 59.513 50.000 3.84 0.00 39.94 2.10
2907 4396 0.523072 CCGATGGTTTCAGGTGCTTG 59.477 55.000 0.00 0.00 0.00 4.01
2925 4414 2.003301 GCTTACTGCTAGTGTGCTTCC 58.997 52.381 0.00 0.00 38.95 3.46
2926 4415 2.670414 CTGCTTACTGCTAGTGTGCTTC 59.330 50.000 0.00 0.00 43.37 3.86
2938 4427 0.693049 AACCCCCTGTCTGCTTACTG 59.307 55.000 0.00 0.00 0.00 2.74
2939 4428 2.337359 TAACCCCCTGTCTGCTTACT 57.663 50.000 0.00 0.00 0.00 2.24
2940 4429 2.919228 CATAACCCCCTGTCTGCTTAC 58.081 52.381 0.00 0.00 0.00 2.34
2944 4433 0.749454 CAGCATAACCCCCTGTCTGC 60.749 60.000 0.00 0.00 36.36 4.26
2947 4436 0.323360 TTGCAGCATAACCCCCTGTC 60.323 55.000 0.00 0.00 0.00 3.51
2951 4440 2.235898 TGAAAATTGCAGCATAACCCCC 59.764 45.455 0.00 0.00 0.00 5.40
2970 4459 4.202192 TGCCACACTGTAATGCAAATTTGA 60.202 37.500 22.31 7.50 0.00 2.69
2971 4460 4.056740 TGCCACACTGTAATGCAAATTTG 58.943 39.130 14.03 14.03 0.00 2.32
2982 4471 9.509956 AAATACTAGTAAAATTGCCACACTGTA 57.490 29.630 6.70 0.00 0.00 2.74
3008 4501 8.537016 GCTTACCATGGTCCATATATACTGTAA 58.463 37.037 23.76 3.59 0.00 2.41
3012 4505 7.568128 TTGCTTACCATGGTCCATATATACT 57.432 36.000 23.76 0.00 0.00 2.12
3018 4511 3.461458 TCCATTGCTTACCATGGTCCATA 59.539 43.478 23.76 0.00 35.74 2.74
3050 4543 3.372206 CAGTGACTTGAAATGGTCGATCC 59.628 47.826 0.00 0.00 35.45 3.36


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

AutoCloner maintained by Alex Coulton.