Multiple sequence alignment - TraesCS4A01G330000

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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 TraesCS4A01G330000 chr4A 100.000 4102 0 0 1 4102 615107167 615103066 0.000000e+00 7576.0
1 TraesCS4A01G330000 chr4A 90.140 1075 63 20 2619 3679 614911347 614910302 0.000000e+00 1358.0
2 TraesCS4A01G330000 chr4A 89.362 188 9 4 3678 3865 614910251 614910075 4.130000e-55 226.0
3 TraesCS4A01G330000 chr4A 87.417 151 16 1 3318 3468 615179078 615178931 1.960000e-38 171.0
4 TraesCS4A01G330000 chr4A 97.297 37 0 1 3783 3818 615103301 615103265 1.230000e-05 62.1
5 TraesCS4A01G330000 chr4A 97.297 37 0 1 3867 3903 615103385 615103350 1.230000e-05 62.1
6 TraesCS4A01G330000 chr5B 94.642 3229 142 11 8 3223 697346935 697343725 0.000000e+00 4975.0
7 TraesCS4A01G330000 chr5B 88.584 911 76 14 2739 3629 697178951 697178049 0.000000e+00 1081.0
8 TraesCS4A01G330000 chr5B 88.188 745 54 14 2360 3076 697184403 697183665 0.000000e+00 857.0
9 TraesCS4A01G330000 chr5B 87.643 437 41 5 2738 3161 697239622 697239186 2.850000e-136 496.0
10 TraesCS4A01G330000 chr5B 94.798 173 9 0 3929 4101 697306101 697305929 1.880000e-68 270.0
11 TraesCS4A01G330000 chr5B 89.535 172 17 1 3931 4102 697176261 697176091 2.480000e-52 217.0
12 TraesCS4A01G330000 chr5B 84.475 219 29 4 3462 3679 697509242 697509028 1.160000e-50 211.0
13 TraesCS4A01G330000 chr5B 90.580 138 8 1 3728 3865 697306265 697306133 1.170000e-40 178.0
14 TraesCS4A01G330000 chr5B 89.344 122 13 0 3499 3620 697527720 697527599 1.970000e-33 154.0
15 TraesCS4A01G330000 chr5B 92.453 106 8 0 3499 3604 697563258 697563153 7.100000e-33 152.0
16 TraesCS4A01G330000 chr5B 86.232 138 19 0 3483 3620 697614182 697614045 2.550000e-32 150.0
17 TraesCS4A01G330000 chr5B 89.362 94 7 3 3499 3589 697333086 697332993 9.320000e-22 115.0
18 TraesCS4A01G330000 chr5B 89.247 93 5 2 3728 3820 697176436 697176349 1.210000e-20 111.0
19 TraesCS4A01G330000 chr5B 96.970 33 1 0 3318 3350 697528693 697528661 5.730000e-04 56.5
20 TraesCS4A01G330000 chr5D 96.622 2664 89 1 8 2671 553470043 553472705 0.000000e+00 4420.0
21 TraesCS4A01G330000 chr5D 90.118 3218 260 16 8 3196 553461054 553457866 0.000000e+00 4128.0
22 TraesCS4A01G330000 chr5D 92.243 1908 130 12 1780 3678 553063784 553065682 0.000000e+00 2687.0
23 TraesCS4A01G330000 chr5D 92.272 854 48 7 2705 3546 553472703 553473550 0.000000e+00 1195.0
24 TraesCS4A01G330000 chr5D 89.272 755 63 10 2360 3099 553509105 553509856 0.000000e+00 929.0
25 TraesCS4A01G330000 chr5D 82.169 673 72 23 2676 3308 553060445 553059781 6.040000e-148 534.0
26 TraesCS4A01G330000 chr5D 94.475 181 10 0 1552 1732 553063594 553063774 3.120000e-71 279.0
27 TraesCS4A01G330000 chr5D 91.852 135 10 1 3929 4062 553473916 553474050 1.950000e-43 187.0
28 TraesCS4A01G330000 chr5D 95.652 69 3 0 3734 3802 553473717 553473785 1.210000e-20 111.0
29 TraesCS4A01G330000 chr2B 72.542 1424 333 39 1216 2598 798129905 798131311 1.060000e-110 411.0


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 TraesCS4A01G330000 chr4A 615103066 615107167 4101 True 2566.733333 7576 98.1980 1 4102 3 chr4A.!!$R3 4101
1 TraesCS4A01G330000 chr4A 614910075 614911347 1272 True 792.000000 1358 89.7510 2619 3865 2 chr4A.!!$R2 1246
2 TraesCS4A01G330000 chr5B 697343725 697346935 3210 True 4975.000000 4975 94.6420 8 3223 1 chr5B.!!$R4 3215
3 TraesCS4A01G330000 chr5B 697183665 697184403 738 True 857.000000 857 88.1880 2360 3076 1 chr5B.!!$R1 716
4 TraesCS4A01G330000 chr5B 697176091 697178951 2860 True 469.666667 1081 89.1220 2739 4102 3 chr5B.!!$R8 1363
5 TraesCS4A01G330000 chr5D 553457866 553461054 3188 True 4128.000000 4128 90.1180 8 3196 1 chr5D.!!$R2 3188
6 TraesCS4A01G330000 chr5D 553063594 553065682 2088 False 1483.000000 2687 93.3590 1552 3678 2 chr5D.!!$F2 2126
7 TraesCS4A01G330000 chr5D 553470043 553474050 4007 False 1478.250000 4420 94.0995 8 4062 4 chr5D.!!$F3 4054
8 TraesCS4A01G330000 chr5D 553509105 553509856 751 False 929.000000 929 89.2720 2360 3099 1 chr5D.!!$F1 739
9 TraesCS4A01G330000 chr5D 553059781 553060445 664 True 534.000000 534 82.1690 2676 3308 1 chr5D.!!$R1 632
10 TraesCS4A01G330000 chr2B 798129905 798131311 1406 False 411.000000 411 72.5420 1216 2598 1 chr2B.!!$F1 1382

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
167 168 1.435515 GACGCTCCGCAATCTCTCT 59.564 57.895 0.0 0.0 0.00 3.10 F
507 508 2.749839 TTGCAGGCACCATACCGC 60.750 61.111 0.0 0.0 0.00 5.68 F
1445 1446 1.859302 TTGTCCCACAACCAGCTTTT 58.141 45.000 0.0 0.0 32.34 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1303 0.318762 CTAGCGTCCTAGGAATGGGC 59.681 60.000 14.65 14.46 37.90 5.36 R
1554 1555 1.005569 TCTAAGCGAAGGGACTCCAGA 59.994 52.381 0.00 0.00 38.49 3.86 R
3374 3477 0.109412 GAACAATGAGCTGCAGGTGC 60.109 55.000 25.60 15.04 42.50 5.01 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
167 168 1.435515 GACGCTCCGCAATCTCTCT 59.564 57.895 0.00 0.00 0.00 3.10
347 348 4.124970 ACTTGGTAAGAAACAACCTCGAC 58.875 43.478 0.00 0.00 36.67 4.20
371 372 5.351948 GAGAGATACCTCCTGCTCTTTTT 57.648 43.478 0.00 0.00 40.30 1.94
507 508 2.749839 TTGCAGGCACCATACCGC 60.750 61.111 0.00 0.00 0.00 5.68
703 704 3.660865 ACCTTAGTTTAGCCGTCAACAG 58.339 45.455 0.00 0.00 0.00 3.16
708 709 6.203338 CCTTAGTTTAGCCGTCAACAGTTTTA 59.797 38.462 0.00 0.00 0.00 1.52
879 880 4.329638 TGGCATTATCCCTTCTTTTGGA 57.670 40.909 0.00 0.00 34.54 3.53
1213 1214 3.953712 TGACATACGTGGACTTGTCAT 57.046 42.857 0.00 0.00 42.46 3.06
1296 1297 9.836864 AACCTCTTCTTGCAAGAAAATAATTTT 57.163 25.926 34.71 20.83 43.84 1.82
1302 1303 9.487790 TTCTTGCAAGAAAATAATTTTAGTGGG 57.512 29.630 34.01 1.16 41.75 4.61
1445 1446 1.859302 TTGTCCCACAACCAGCTTTT 58.141 45.000 0.00 0.00 32.34 2.27
1554 1555 2.496070 TGCTCTAGGTGCTTGTATTCGT 59.504 45.455 9.39 0.00 0.00 3.85
1669 1670 2.599848 CGAAACAACTTGAGCGGTGAAG 60.600 50.000 12.38 12.38 0.00 3.02
1916 1923 4.426112 GGCGGCTCTTGCTTTGGC 62.426 66.667 0.00 0.00 39.59 4.52
2085 2092 1.749033 CTCAGGGGCTTACGGATCC 59.251 63.158 0.00 0.00 0.00 3.36
2532 2559 6.937465 AGTTCCTTCAAAGTCATAACTCTTCC 59.063 38.462 0.00 0.00 33.48 3.46
2580 2615 2.243221 AGGACCAAGAGGATCAATTGGG 59.757 50.000 20.53 8.52 42.81 4.12
2610 2645 8.500753 TTGCACCAGGTAAACATTTACTATAG 57.499 34.615 12.90 0.00 42.00 1.31
2667 2703 9.801873 TTCAAGTTTCACTTTTCCTTTATTCAG 57.198 29.630 0.00 0.00 36.03 3.02
2918 2991 8.243961 AGATACTTGATCCTAATATCATCGGG 57.756 38.462 0.00 0.00 35.84 5.14
3032 3117 0.713883 CACCAAAAGATCGACCGACG 59.286 55.000 0.00 0.00 44.09 5.12
3079 3164 5.584649 TCTCCGCAATCAAACGAGAATATTT 59.415 36.000 0.00 0.00 0.00 1.40
3128 3215 5.677612 CACTTTTGTTTTGTTCGCGTGTATA 59.322 36.000 5.77 0.00 0.00 1.47
3131 3218 6.661982 TTTGTTTTGTTCGCGTGTATATTG 57.338 33.333 5.77 0.00 0.00 1.90
3145 3236 6.401688 GCGTGTATATTGCAAGTGAGTTGTAA 60.402 38.462 4.94 6.01 43.83 2.41
3157 3248 7.254590 GCAAGTGAGTTGTAATCTATGCTTAGG 60.255 40.741 6.78 0.00 38.55 2.69
3214 3306 3.617288 GCCTTTATGTTGGGCTTCTTTGG 60.617 47.826 0.00 0.00 42.31 3.28
3223 3322 5.129485 TGTTGGGCTTCTTTGGATTTTTGTA 59.871 36.000 0.00 0.00 0.00 2.41
3275 3378 4.218417 GCCAATCCACTGTGTGATAAAGTT 59.782 41.667 7.08 0.00 35.23 2.66
3284 3387 4.556233 TGTGTGATAAAGTTCGGACTGAG 58.444 43.478 0.00 0.00 35.91 3.35
3285 3388 3.927142 GTGTGATAAAGTTCGGACTGAGG 59.073 47.826 0.00 0.00 35.91 3.86
3289 3392 5.120363 GTGATAAAGTTCGGACTGAGGAAAC 59.880 44.000 0.00 0.00 35.91 2.78
3347 3450 9.334693 GTTGTCTGATTTATTCTGAATGTGTTC 57.665 33.333 13.01 5.58 34.50 3.18
3497 3614 8.618677 CATGATATTACAGTGTGAATTGCTCTT 58.381 33.333 5.88 0.00 0.00 2.85
3542 3684 5.468072 GCATCAGGGCATAGGAATATATTCG 59.532 44.000 17.25 6.56 37.67 3.34
3546 3688 8.141298 TCAGGGCATAGGAATATATTCGTTAA 57.859 34.615 22.01 8.98 37.67 2.01
3551 3693 8.038944 GGCATAGGAATATATTCGTTAACCTGA 58.961 37.037 22.01 6.51 37.67 3.86
3581 3723 4.602107 TGAATTTCTGAGGGCAATGATGA 58.398 39.130 0.00 0.00 0.00 2.92
3589 3731 7.320384 TCTGAGGGCAATGATGATAGATTTA 57.680 36.000 0.00 0.00 0.00 1.40
3634 3776 6.501781 GTTTCAGGCATAAGATTTGATCAGG 58.498 40.000 0.00 0.00 0.00 3.86
3638 5314 3.255149 GGCATAAGATTTGATCAGGCTGG 59.745 47.826 15.73 0.00 0.00 4.85
3639 5315 4.139786 GCATAAGATTTGATCAGGCTGGA 58.860 43.478 15.73 1.60 0.00 3.86
3642 5318 3.557228 AGATTTGATCAGGCTGGAGAC 57.443 47.619 15.73 4.59 0.00 3.36
3644 5320 3.265221 AGATTTGATCAGGCTGGAGACAA 59.735 43.478 15.73 12.46 42.06 3.18
3654 5330 3.073650 AGGCTGGAGACAAAAGATTCACT 59.926 43.478 0.00 0.00 42.06 3.41
3655 5331 3.190118 GGCTGGAGACAAAAGATTCACTG 59.810 47.826 0.00 0.00 42.06 3.66
3661 5337 5.763204 GGAGACAAAAGATTCACTGGTGTTA 59.237 40.000 0.53 0.00 30.05 2.41
3667 5343 6.619801 AAAGATTCACTGGTGTTACTTGTC 57.380 37.500 0.53 0.00 0.00 3.18
3679 5355 2.163818 TACTTGTCGCTTGAAGGGTG 57.836 50.000 9.15 1.91 0.00 4.61
3682 5358 0.759959 TTGTCGCTTGAAGGGTGGTA 59.240 50.000 9.15 0.00 0.00 3.25
3683 5359 0.320374 TGTCGCTTGAAGGGTGGTAG 59.680 55.000 9.15 0.00 0.00 3.18
3684 5360 0.320697 GTCGCTTGAAGGGTGGTAGT 59.679 55.000 9.15 0.00 0.00 2.73
3685 5361 0.320374 TCGCTTGAAGGGTGGTAGTG 59.680 55.000 9.15 0.00 0.00 2.74
3686 5362 0.673644 CGCTTGAAGGGTGGTAGTGG 60.674 60.000 0.53 0.00 0.00 4.00
3688 5364 1.626825 GCTTGAAGGGTGGTAGTGGTA 59.373 52.381 0.00 0.00 0.00 3.25
3689 5365 2.354805 GCTTGAAGGGTGGTAGTGGTAG 60.355 54.545 0.00 0.00 0.00 3.18
3690 5366 2.708037 TGAAGGGTGGTAGTGGTAGT 57.292 50.000 0.00 0.00 0.00 2.73
3691 5367 2.253610 TGAAGGGTGGTAGTGGTAGTG 58.746 52.381 0.00 0.00 0.00 2.74
3692 5368 1.553704 GAAGGGTGGTAGTGGTAGTGG 59.446 57.143 0.00 0.00 0.00 4.00
3693 5369 0.908180 AGGGTGGTAGTGGTAGTGGC 60.908 60.000 0.00 0.00 0.00 5.01
3694 5370 1.196104 GGGTGGTAGTGGTAGTGGCA 61.196 60.000 0.00 0.00 0.00 4.92
3695 5371 0.249398 GGTGGTAGTGGTAGTGGCAG 59.751 60.000 0.00 0.00 0.00 4.85
3696 5372 0.974383 GTGGTAGTGGTAGTGGCAGT 59.026 55.000 0.00 0.00 0.00 4.40
3697 5373 0.973632 TGGTAGTGGTAGTGGCAGTG 59.026 55.000 4.76 0.00 0.00 3.66
3698 5374 0.974383 GGTAGTGGTAGTGGCAGTGT 59.026 55.000 4.76 0.00 0.00 3.55
3699 5375 1.337823 GGTAGTGGTAGTGGCAGTGTG 60.338 57.143 4.76 0.00 0.00 3.82
3700 5376 1.343465 GTAGTGGTAGTGGCAGTGTGT 59.657 52.381 4.76 0.00 0.00 3.72
3701 5377 0.393077 AGTGGTAGTGGCAGTGTGTC 59.607 55.000 4.76 0.00 0.00 3.67
3702 5378 0.105964 GTGGTAGTGGCAGTGTGTCA 59.894 55.000 4.76 0.00 0.00 3.58
3703 5379 1.055849 TGGTAGTGGCAGTGTGTCAT 58.944 50.000 4.76 0.00 33.03 3.06
3707 5413 3.306780 GGTAGTGGCAGTGTGTCATAGTT 60.307 47.826 4.76 0.00 33.03 2.24
3721 5449 4.096231 TGTCATAGTTGCAGCGCATAAATT 59.904 37.500 11.47 0.00 38.76 1.82
3722 5450 5.295540 TGTCATAGTTGCAGCGCATAAATTA 59.704 36.000 11.47 1.82 38.76 1.40
3723 5451 5.621228 GTCATAGTTGCAGCGCATAAATTAC 59.379 40.000 11.47 0.00 38.76 1.89
3724 5452 5.527214 TCATAGTTGCAGCGCATAAATTACT 59.473 36.000 11.47 5.98 38.76 2.24
3725 5453 4.278678 AGTTGCAGCGCATAAATTACTC 57.721 40.909 11.47 0.00 38.76 2.59
3726 5454 3.029074 GTTGCAGCGCATAAATTACTCG 58.971 45.455 11.47 0.00 38.76 4.18
3732 5460 5.423717 CAGCGCATAAATTACTCGTAGTTG 58.576 41.667 11.47 0.00 0.00 3.16
3800 5528 7.338196 TCAATTTAAGCCCAATTCAACGAGATA 59.662 33.333 0.00 0.00 0.00 1.98
3801 5529 6.431198 TTTAAGCCCAATTCAACGAGATAC 57.569 37.500 0.00 0.00 0.00 2.24
3802 5530 3.914426 AGCCCAATTCAACGAGATACT 57.086 42.857 0.00 0.00 0.00 2.12
3803 5531 3.535561 AGCCCAATTCAACGAGATACTG 58.464 45.455 0.00 0.00 0.00 2.74
3858 5625 4.323104 GCCCAGTGAATTAGTTGAGAGACT 60.323 45.833 0.00 0.00 0.00 3.24
3868 5635 7.576861 ATTAGTTGAGAGACTAACTAGGAGC 57.423 40.000 0.00 0.00 42.92 4.70
3869 5636 4.274978 AGTTGAGAGACTAACTAGGAGCC 58.725 47.826 0.00 0.00 35.50 4.70
3870 5637 3.300239 TGAGAGACTAACTAGGAGCCC 57.700 52.381 0.00 0.00 0.00 5.19
3872 5639 3.011369 TGAGAGACTAACTAGGAGCCCAA 59.989 47.826 0.00 0.00 0.00 4.12
3874 5641 4.625963 AGAGACTAACTAGGAGCCCAATT 58.374 43.478 0.00 0.00 0.00 2.32
3877 5644 4.783227 AGACTAACTAGGAGCCCAATTCAA 59.217 41.667 0.00 0.00 0.00 2.69
3878 5645 4.844884 ACTAACTAGGAGCCCAATTCAAC 58.155 43.478 0.00 0.00 0.00 3.18
3879 5646 2.403252 ACTAGGAGCCCAATTCAACG 57.597 50.000 0.00 0.00 0.00 4.10
3883 5650 1.561542 AGGAGCCCAATTCAACGAGAT 59.438 47.619 0.00 0.00 0.00 2.75
3884 5651 2.771943 AGGAGCCCAATTCAACGAGATA 59.228 45.455 0.00 0.00 0.00 1.98
3885 5652 2.872858 GGAGCCCAATTCAACGAGATAC 59.127 50.000 0.00 0.00 0.00 2.24
3886 5653 3.432326 GGAGCCCAATTCAACGAGATACT 60.432 47.826 0.00 0.00 0.00 2.12
3888 5655 3.055094 AGCCCAATTCAACGAGATACTGT 60.055 43.478 0.00 0.00 0.00 3.55
3889 5656 4.161565 AGCCCAATTCAACGAGATACTGTA 59.838 41.667 0.00 0.00 0.00 2.74
3890 5657 4.270325 GCCCAATTCAACGAGATACTGTAC 59.730 45.833 0.00 0.00 0.00 2.90
3891 5658 4.809426 CCCAATTCAACGAGATACTGTACC 59.191 45.833 0.00 0.00 0.00 3.34
3897 5664 2.681848 AACGAGATACTGTACCTCGGTG 59.318 50.000 29.45 8.44 46.93 4.94
3898 5665 2.286872 CGAGATACTGTACCTCGGTGT 58.713 52.381 21.27 0.00 44.11 4.16
3901 5668 4.083961 CGAGATACTGTACCTCGGTGTATG 60.084 50.000 21.27 0.00 44.11 2.39
3902 5669 3.568853 AGATACTGTACCTCGGTGTATGC 59.431 47.826 0.00 0.00 36.91 3.14
3905 5672 2.100916 ACTGTACCTCGGTGTATGCATC 59.899 50.000 0.19 0.00 33.92 3.91
3906 5673 2.100749 CTGTACCTCGGTGTATGCATCA 59.899 50.000 0.19 0.00 0.00 3.07
3907 5674 2.498078 TGTACCTCGGTGTATGCATCAA 59.502 45.455 0.19 0.00 0.00 2.57
3908 5675 3.133901 TGTACCTCGGTGTATGCATCAAT 59.866 43.478 0.19 0.00 0.00 2.57
3909 5676 3.281727 ACCTCGGTGTATGCATCAATT 57.718 42.857 0.19 0.00 0.00 2.32
3910 5677 3.620488 ACCTCGGTGTATGCATCAATTT 58.380 40.909 0.19 0.00 0.00 1.82
3911 5678 4.776349 ACCTCGGTGTATGCATCAATTTA 58.224 39.130 0.19 0.00 0.00 1.40
3912 5679 5.189928 ACCTCGGTGTATGCATCAATTTAA 58.810 37.500 0.19 0.00 0.00 1.52
3913 5680 5.296780 ACCTCGGTGTATGCATCAATTTAAG 59.703 40.000 0.19 0.00 0.00 1.85
3914 5681 5.296780 CCTCGGTGTATGCATCAATTTAAGT 59.703 40.000 0.19 0.00 0.00 2.24
3915 5682 6.183360 CCTCGGTGTATGCATCAATTTAAGTT 60.183 38.462 0.19 0.00 0.00 2.66
3916 5683 6.781138 TCGGTGTATGCATCAATTTAAGTTC 58.219 36.000 0.19 0.00 0.00 3.01
3917 5684 6.372937 TCGGTGTATGCATCAATTTAAGTTCA 59.627 34.615 0.19 0.00 0.00 3.18
3918 5685 7.026562 CGGTGTATGCATCAATTTAAGTTCAA 58.973 34.615 0.19 0.00 0.00 2.69
3919 5686 7.701924 CGGTGTATGCATCAATTTAAGTTCAAT 59.298 33.333 0.19 0.00 0.00 2.57
3920 5687 9.369904 GGTGTATGCATCAATTTAAGTTCAATT 57.630 29.630 0.19 0.00 0.00 2.32
3925 5692 8.883954 TGCATCAATTTAAGTTCAATTCAACA 57.116 26.923 0.00 0.00 0.00 3.33
3926 5693 8.763356 TGCATCAATTTAAGTTCAATTCAACAC 58.237 29.630 0.00 0.00 0.00 3.32
3927 5694 7.946237 GCATCAATTTAAGTTCAATTCAACACG 59.054 33.333 0.00 0.00 0.00 4.49
3953 5720 7.678194 AAGTTCAATTCAACACGTACATTTG 57.322 32.000 0.00 0.00 0.00 2.32
3973 5740 1.628846 GTCAGGACCCAGGAGCTAAAA 59.371 52.381 0.00 0.00 0.00 1.52
3974 5741 1.909302 TCAGGACCCAGGAGCTAAAAG 59.091 52.381 0.00 0.00 0.00 2.27
3979 5746 3.118702 GGACCCAGGAGCTAAAAGTAGAC 60.119 52.174 0.00 0.00 0.00 2.59
4010 5777 1.765314 CCATTCGGAGAGGAACAGGAT 59.235 52.381 0.00 0.00 38.43 3.24
4027 5794 2.641439 GATCACCGGAGCAGCTGAGG 62.641 65.000 20.43 16.35 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.746671 CCTGCTCAGCTGCCACAG 60.747 66.667 9.47 15.17 34.12 3.66
4 5 3.124051 AACCTGCTCAGCTGCCACA 62.124 57.895 9.47 5.91 0.00 4.17
5 6 2.282040 AACCTGCTCAGCTGCCAC 60.282 61.111 9.47 0.76 0.00 5.01
6 7 2.281970 CAACCTGCTCAGCTGCCA 60.282 61.111 9.47 7.78 0.00 4.92
116 117 4.140924 TCTGGGATATCTCCACTGAGCTTA 60.141 45.833 0.00 0.00 44.08 3.09
167 168 1.160946 TGCGAGCAAGGCGTAAAACA 61.161 50.000 0.00 0.00 0.00 2.83
239 240 2.037121 TGCGAGGATGACAGAAACAAGA 59.963 45.455 0.00 0.00 0.00 3.02
507 508 4.395231 GGAAGAAAAATTACCCAGAGTCGG 59.605 45.833 0.00 0.00 0.00 4.79
651 652 5.192927 TGAAGACATGTTGAATATGGGGAC 58.807 41.667 0.00 0.00 0.00 4.46
703 704 6.649141 GTCAAATGGAAGTTCCCCAATAAAAC 59.351 38.462 19.42 4.12 37.22 2.43
708 709 3.855668 TGTCAAATGGAAGTTCCCCAAT 58.144 40.909 19.42 3.39 37.22 3.16
779 780 2.179427 CAGGGATTTTTCCTCCAACCC 58.821 52.381 0.00 0.00 34.24 4.11
879 880 9.654919 ATTAGCTCTTCTAGGTTAGAAAGAGAT 57.345 33.333 16.73 13.83 43.63 2.75
1213 1214 1.070134 CTGTCCGGAAAGTCTGTTCCA 59.930 52.381 14.07 0.00 46.45 3.53
1296 1297 0.645496 TCCTAGGAATGGGCCCACTA 59.355 55.000 31.51 22.82 0.00 2.74
1302 1303 0.318762 CTAGCGTCCTAGGAATGGGC 59.681 60.000 14.65 14.46 37.90 5.36
1554 1555 1.005569 TCTAAGCGAAGGGACTCCAGA 59.994 52.381 0.00 0.00 38.49 3.86
1669 1670 3.296854 AGGACTGGAAAAAGTTTGGGAC 58.703 45.455 0.00 0.00 0.00 4.46
1916 1923 5.545658 AAATACTACGCATGACAAACAGG 57.454 39.130 0.00 0.00 0.00 4.00
2085 2092 5.125097 AGACTCAAGTACACCCTTGTATACG 59.875 44.000 0.00 0.00 40.40 3.06
2532 2559 8.011106 GCTAAGCTCGTAGAAGTAATAGTACTG 58.989 40.741 5.39 0.00 39.79 2.74
2580 2615 5.385509 AATGTTTACCTGGTGCAATGTAC 57.614 39.130 10.23 0.00 0.00 2.90
2918 2991 1.156736 CATGGTCCACAACTTCGTCC 58.843 55.000 0.00 0.00 0.00 4.79
3032 3117 2.654404 GCGTAGACGTCCGGCATC 60.654 66.667 13.01 0.00 42.22 3.91
3079 3164 0.672091 TTCCTTGACGCGCAATGCTA 60.672 50.000 5.73 0.00 43.27 3.49
3128 3215 6.600822 AGCATAGATTACAACTCACTTGCAAT 59.399 34.615 0.00 0.00 32.41 3.56
3131 3218 6.428385 AAGCATAGATTACAACTCACTTGC 57.572 37.500 0.00 0.00 32.41 4.01
3145 3236 3.713764 ACCTGAGCAACCTAAGCATAGAT 59.286 43.478 0.00 0.00 0.00 1.98
3157 3248 1.070758 TCTTCCAGTCACCTGAGCAAC 59.929 52.381 0.00 0.00 41.50 4.17
3214 3306 9.151471 TGAAGTATCAGCAGTACTACAAAAATC 57.849 33.333 0.00 0.00 32.34 2.17
3275 3378 1.691976 ACATGTGTTTCCTCAGTCCGA 59.308 47.619 0.00 0.00 0.00 4.55
3284 3387 2.227388 CAGCCTGAGAACATGTGTTTCC 59.773 50.000 0.00 0.00 38.56 3.13
3285 3388 2.351157 GCAGCCTGAGAACATGTGTTTC 60.351 50.000 0.00 0.00 38.56 2.78
3289 3392 0.803117 CTGCAGCCTGAGAACATGTG 59.197 55.000 0.00 0.00 0.00 3.21
3350 3453 8.268605 TGCCTGAACATATTTACACCTGTATAA 58.731 33.333 0.00 0.00 0.00 0.98
3357 3460 4.096382 CAGGTGCCTGAACATATTTACACC 59.904 45.833 12.66 0.00 46.30 4.16
3359 3462 3.694072 GCAGGTGCCTGAACATATTTACA 59.306 43.478 21.34 0.00 46.30 2.41
3364 3467 2.020694 GCTGCAGGTGCCTGAACATAT 61.021 52.381 21.34 0.00 46.30 1.78
3374 3477 0.109412 GAACAATGAGCTGCAGGTGC 60.109 55.000 25.60 15.04 42.50 5.01
3497 3614 7.445096 TGATGCTAGACAAAACAGATTTCTCAA 59.555 33.333 0.00 0.00 0.00 3.02
3542 3684 7.805071 CAGAAATTCAGAACATGTCAGGTTAAC 59.195 37.037 2.27 0.00 0.00 2.01
3546 3688 5.624159 TCAGAAATTCAGAACATGTCAGGT 58.376 37.500 0.00 0.00 0.00 4.00
3551 3693 3.760684 GCCCTCAGAAATTCAGAACATGT 59.239 43.478 0.00 0.00 0.00 3.21
3581 3723 7.212274 GGCATGTTTCCATTTGCTAAATCTAT 58.788 34.615 0.00 0.00 0.00 1.98
3589 3731 0.968405 ACGGCATGTTTCCATTTGCT 59.032 45.000 0.00 0.00 0.00 3.91
3606 3748 4.092821 TCAAATCTTATGCCTGAAACGACG 59.907 41.667 0.00 0.00 0.00 5.12
3608 3750 5.879777 TGATCAAATCTTATGCCTGAAACGA 59.120 36.000 0.00 0.00 0.00 3.85
3620 3762 4.471025 TGTCTCCAGCCTGATCAAATCTTA 59.529 41.667 0.00 0.00 0.00 2.10
3634 3776 3.190118 CCAGTGAATCTTTTGTCTCCAGC 59.810 47.826 0.00 0.00 0.00 4.85
3638 5314 5.757850 AACACCAGTGAATCTTTTGTCTC 57.242 39.130 4.48 0.00 0.00 3.36
3639 5315 6.357367 AGTAACACCAGTGAATCTTTTGTCT 58.643 36.000 4.48 0.00 0.00 3.41
3642 5318 6.795399 ACAAGTAACACCAGTGAATCTTTTG 58.205 36.000 4.48 4.41 0.00 2.44
3644 5320 5.236478 CGACAAGTAACACCAGTGAATCTTT 59.764 40.000 4.48 0.00 0.00 2.52
3654 5330 2.605837 TCAAGCGACAAGTAACACCA 57.394 45.000 0.00 0.00 0.00 4.17
3655 5331 2.223377 CCTTCAAGCGACAAGTAACACC 59.777 50.000 0.00 0.00 0.00 4.16
3661 5337 0.535102 CCACCCTTCAAGCGACAAGT 60.535 55.000 0.00 0.00 0.00 3.16
3667 5343 0.673644 CCACTACCACCCTTCAAGCG 60.674 60.000 0.00 0.00 0.00 4.68
3679 5355 0.974383 ACACTGCCACTACCACTACC 59.026 55.000 0.00 0.00 0.00 3.18
3682 5358 0.393077 GACACACTGCCACTACCACT 59.607 55.000 0.00 0.00 0.00 4.00
3683 5359 0.105964 TGACACACTGCCACTACCAC 59.894 55.000 0.00 0.00 0.00 4.16
3684 5360 1.055849 ATGACACACTGCCACTACCA 58.944 50.000 0.00 0.00 0.00 3.25
3685 5361 2.233922 ACTATGACACACTGCCACTACC 59.766 50.000 0.00 0.00 0.00 3.18
3686 5362 3.594603 ACTATGACACACTGCCACTAC 57.405 47.619 0.00 0.00 0.00 2.73
3688 5364 2.771089 CAACTATGACACACTGCCACT 58.229 47.619 0.00 0.00 0.00 4.00
3689 5365 1.197721 GCAACTATGACACACTGCCAC 59.802 52.381 0.00 0.00 0.00 5.01
3690 5366 1.202746 TGCAACTATGACACACTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
3691 5367 1.466167 CTGCAACTATGACACACTGCC 59.534 52.381 0.00 0.00 0.00 4.85
3692 5368 1.135859 GCTGCAACTATGACACACTGC 60.136 52.381 0.00 0.00 0.00 4.40
3693 5369 1.127397 CGCTGCAACTATGACACACTG 59.873 52.381 0.00 0.00 0.00 3.66
3694 5370 1.432514 CGCTGCAACTATGACACACT 58.567 50.000 0.00 0.00 0.00 3.55
3695 5371 0.179215 GCGCTGCAACTATGACACAC 60.179 55.000 0.00 0.00 0.00 3.82
3696 5372 0.602372 TGCGCTGCAACTATGACACA 60.602 50.000 9.73 0.00 34.76 3.72
3697 5373 0.729116 ATGCGCTGCAACTATGACAC 59.271 50.000 9.73 0.00 43.62 3.67
3698 5374 2.307934 TATGCGCTGCAACTATGACA 57.692 45.000 9.73 0.00 43.62 3.58
3699 5375 3.673746 TTTATGCGCTGCAACTATGAC 57.326 42.857 9.73 0.00 43.62 3.06
3700 5376 4.898829 AATTTATGCGCTGCAACTATGA 57.101 36.364 9.73 0.00 43.62 2.15
3701 5377 5.751680 AGTAATTTATGCGCTGCAACTATG 58.248 37.500 9.73 0.00 43.62 2.23
3702 5378 5.333339 CGAGTAATTTATGCGCTGCAACTAT 60.333 40.000 9.73 0.00 43.62 2.12
3703 5379 4.026062 CGAGTAATTTATGCGCTGCAACTA 60.026 41.667 9.73 0.00 43.62 2.24
3707 5413 2.276201 ACGAGTAATTTATGCGCTGCA 58.724 42.857 9.73 5.73 44.86 4.41
3721 5449 6.694877 ATGCTAACATCTCAACTACGAGTA 57.305 37.500 0.00 0.00 34.46 2.59
3722 5450 5.584253 ATGCTAACATCTCAACTACGAGT 57.416 39.130 0.00 0.00 34.46 4.18
3723 5451 6.036470 TCAATGCTAACATCTCAACTACGAG 58.964 40.000 0.00 0.00 34.62 4.18
3724 5452 5.961272 TCAATGCTAACATCTCAACTACGA 58.039 37.500 0.00 0.00 34.62 3.43
3725 5453 6.531594 TCTTCAATGCTAACATCTCAACTACG 59.468 38.462 0.00 0.00 34.62 3.51
3726 5454 7.547370 ACTCTTCAATGCTAACATCTCAACTAC 59.453 37.037 0.00 0.00 34.62 2.73
3732 5460 5.871524 TGACACTCTTCAATGCTAACATCTC 59.128 40.000 0.00 0.00 34.62 2.75
3800 5528 0.756903 AAGCAACACCGAGGTACAGT 59.243 50.000 0.00 0.00 0.00 3.55
3801 5529 1.148310 CAAGCAACACCGAGGTACAG 58.852 55.000 0.00 0.00 0.00 2.74
3802 5530 0.466543 ACAAGCAACACCGAGGTACA 59.533 50.000 0.00 0.00 0.00 2.90
3803 5531 0.865769 CACAAGCAACACCGAGGTAC 59.134 55.000 0.00 0.00 0.00 3.34
3842 5587 8.132995 GCTCCTAGTTAGTCTCTCAACTAATTC 58.867 40.741 0.34 0.00 42.16 2.17
3858 5625 3.516300 TCGTTGAATTGGGCTCCTAGTTA 59.484 43.478 0.00 0.00 0.00 2.24
3868 5635 4.809426 GGTACAGTATCTCGTTGAATTGGG 59.191 45.833 0.00 0.00 0.00 4.12
3869 5636 5.661458 AGGTACAGTATCTCGTTGAATTGG 58.339 41.667 0.00 0.00 0.00 3.16
3870 5637 6.814076 GAGGTACAGTATCTCGTTGAATTG 57.186 41.667 5.04 0.00 0.00 2.32
3879 5646 4.320348 GCATACACCGAGGTACAGTATCTC 60.320 50.000 10.53 10.53 32.52 2.75
3883 5650 2.725637 TGCATACACCGAGGTACAGTA 58.274 47.619 0.00 0.00 0.00 2.74
3884 5651 1.552578 TGCATACACCGAGGTACAGT 58.447 50.000 0.00 0.00 0.00 3.55
3885 5652 2.100749 TGATGCATACACCGAGGTACAG 59.899 50.000 0.00 0.00 0.00 2.74
3886 5653 2.104170 TGATGCATACACCGAGGTACA 58.896 47.619 0.00 0.00 0.00 2.90
3888 5655 4.415881 AATTGATGCATACACCGAGGTA 57.584 40.909 0.00 0.00 0.00 3.08
3889 5656 3.281727 AATTGATGCATACACCGAGGT 57.718 42.857 0.00 0.00 0.00 3.85
3890 5657 5.296780 ACTTAAATTGATGCATACACCGAGG 59.703 40.000 0.00 0.00 0.00 4.63
3891 5658 6.363577 ACTTAAATTGATGCATACACCGAG 57.636 37.500 0.00 0.00 0.00 4.63
3894 5661 8.931385 ATTGAACTTAAATTGATGCATACACC 57.069 30.769 0.00 0.00 0.00 4.16
3901 5668 7.946237 CGTGTTGAATTGAACTTAAATTGATGC 59.054 33.333 9.24 0.00 0.00 3.91
3902 5669 8.967218 ACGTGTTGAATTGAACTTAAATTGATG 58.033 29.630 9.24 0.00 0.00 3.07
3908 5675 9.493206 GAACTTACGTGTTGAATTGAACTTAAA 57.507 29.630 9.24 0.00 0.00 1.52
3909 5676 8.666573 TGAACTTACGTGTTGAATTGAACTTAA 58.333 29.630 9.24 3.86 0.00 1.85
3910 5677 8.199176 TGAACTTACGTGTTGAATTGAACTTA 57.801 30.769 9.24 0.00 0.00 2.24
3911 5678 7.079182 TGAACTTACGTGTTGAATTGAACTT 57.921 32.000 9.24 0.00 0.00 2.66
3912 5679 6.671614 TGAACTTACGTGTTGAATTGAACT 57.328 33.333 9.24 0.00 0.00 3.01
3913 5680 7.908193 ATTGAACTTACGTGTTGAATTGAAC 57.092 32.000 0.00 0.27 31.59 3.18
3914 5681 8.184848 TGAATTGAACTTACGTGTTGAATTGAA 58.815 29.630 16.81 6.36 41.35 2.69
3915 5682 7.698628 TGAATTGAACTTACGTGTTGAATTGA 58.301 30.769 16.81 8.99 41.35 2.57
3916 5683 7.906611 TGAATTGAACTTACGTGTTGAATTG 57.093 32.000 16.81 0.00 41.35 2.32
3917 5684 7.971168 TGTTGAATTGAACTTACGTGTTGAATT 59.029 29.630 13.38 13.38 42.96 2.17
3918 5685 7.431084 GTGTTGAATTGAACTTACGTGTTGAAT 59.569 33.333 9.24 0.00 35.80 2.57
3919 5686 6.743627 GTGTTGAATTGAACTTACGTGTTGAA 59.256 34.615 9.24 0.00 0.00 2.69
3920 5687 6.252281 GTGTTGAATTGAACTTACGTGTTGA 58.748 36.000 9.24 0.00 0.00 3.18
3921 5688 5.168856 CGTGTTGAATTGAACTTACGTGTTG 59.831 40.000 9.24 0.00 0.00 3.33
3922 5689 5.163834 ACGTGTTGAATTGAACTTACGTGTT 60.164 36.000 19.92 0.00 37.19 3.32
3923 5690 4.330620 ACGTGTTGAATTGAACTTACGTGT 59.669 37.500 19.92 2.91 37.19 4.49
3924 5691 4.828704 ACGTGTTGAATTGAACTTACGTG 58.171 39.130 19.92 3.78 37.19 4.49
3925 5692 5.519566 TGTACGTGTTGAATTGAACTTACGT 59.480 36.000 22.60 22.60 39.95 3.57
3926 5693 5.965202 TGTACGTGTTGAATTGAACTTACG 58.035 37.500 15.56 15.56 33.66 3.18
3927 5694 8.678510 CAAATGTACGTGTTGAATTGAACTTAC 58.321 33.333 9.24 8.12 0.00 2.34
3953 5720 1.276622 TTTAGCTCCTGGGTCCTGAC 58.723 55.000 0.00 0.00 0.00 3.51
3973 5740 2.425143 TGGATCGGGTAACGTCTACT 57.575 50.000 0.00 0.00 44.69 2.57
3974 5741 3.636381 GAATGGATCGGGTAACGTCTAC 58.364 50.000 0.00 0.00 44.69 2.59
4010 5777 3.385384 CCTCAGCTGCTCCGGTGA 61.385 66.667 9.47 0.00 38.92 4.02


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

AutoCloner maintained by Alex Coulton.