Multiple sequence alignment - TraesCS1D01G175700

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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 TraesCS1D01G175700 chr1D 100.000 3527 0 0 1 3527 250071792 250068266 0.000000e+00 6514.0
1 TraesCS1D01G175700 chr1D 87.334 1579 180 11 961 2521 249755674 249754098 0.000000e+00 1790.0
2 TraesCS1D01G175700 chr1D 81.652 1477 218 33 1079 2519 442798159 442799618 0.000000e+00 1177.0
3 TraesCS1D01G175700 chr1D 80.628 1466 237 40 1078 2515 389489295 389490741 0.000000e+00 1090.0
4 TraesCS1D01G175700 chr1D 80.287 1461 233 32 1087 2500 250139011 250137559 0.000000e+00 1051.0
5 TraesCS1D01G175700 chr1D 93.258 89 5 1 202 289 178657746 178657834 2.860000e-26 130.0
6 TraesCS1D01G175700 chr1B 94.698 2282 75 21 642 2905 364504550 364506803 0.000000e+00 3502.0
7 TraesCS1D01G175700 chr1B 81.122 1462 222 41 1087 2515 522744770 522743330 0.000000e+00 1122.0
8 TraesCS1D01G175700 chr1B 80.598 1438 227 28 1092 2485 364423143 364424572 0.000000e+00 1062.0
9 TraesCS1D01G175700 chr1B 91.356 590 51 0 1932 2521 364812164 364812753 0.000000e+00 808.0
10 TraesCS1D01G175700 chr1B 83.668 796 110 11 960 1737 364811158 364811951 0.000000e+00 732.0
11 TraesCS1D01G175700 chr1B 86.435 317 18 9 287 586 364504241 364504549 1.220000e-84 324.0
12 TraesCS1D01G175700 chr1B 90.909 154 12 2 137 289 364503346 364503498 4.620000e-49 206.0
13 TraesCS1D01G175700 chr1A 95.032 2214 78 13 489 2685 319889901 319887703 0.000000e+00 3450.0
14 TraesCS1D01G175700 chr1A 87.223 1581 181 11 961 2521 319447542 319445963 0.000000e+00 1781.0
15 TraesCS1D01G175700 chr1A 80.518 1468 238 41 1078 2515 488097689 488099138 0.000000e+00 1083.0
16 TraesCS1D01G175700 chr1A 80.736 1168 172 31 1378 2496 320155707 320154544 0.000000e+00 861.0
17 TraesCS1D01G175700 chr1A 91.329 519 19 9 1 505 319890708 319890202 0.000000e+00 686.0
18 TraesCS1D01G175700 chr1A 84.055 439 36 15 2983 3410 319887114 319886699 3.300000e-105 392.0
19 TraesCS1D01G175700 chr1A 93.119 218 9 6 2752 2966 319887404 319887190 7.350000e-82 315.0
20 TraesCS1D01G175700 chr2D 92.982 114 6 1 3414 3527 416404399 416404510 7.830000e-37 165.0
21 TraesCS1D01G175700 chr2D 92.045 88 6 1 200 286 322238263 322238350 4.780000e-24 122.0
22 TraesCS1D01G175700 chr2D 87.013 77 5 1 3451 3527 644344098 644344169 8.110000e-12 82.4
23 TraesCS1D01G175700 chr5D 95.604 91 4 0 3437 3527 495306827 495306737 2.840000e-31 147.0
24 TraesCS1D01G175700 chr5D 93.182 88 5 1 203 289 511515605 511515518 1.030000e-25 128.0
25 TraesCS1D01G175700 chr2A 96.471 85 3 0 3443 3527 606818280 606818364 1.320000e-29 141.0
26 TraesCS1D01G175700 chr6D 92.784 97 5 2 194 289 295562900 295562805 4.750000e-29 139.0
27 TraesCS1D01G175700 chrUn 97.403 77 2 0 3451 3527 132044773 132044849 7.940000e-27 132.0
28 TraesCS1D01G175700 chrUn 100.000 28 0 0 3425 3452 132044758 132044785 6.000000e-03 52.8
29 TraesCS1D01G175700 chr2B 88.596 114 6 2 3414 3527 488202988 488203094 7.940000e-27 132.0
30 TraesCS1D01G175700 chr3B 93.182 88 5 1 203 289 13360882 13360795 1.030000e-25 128.0
31 TraesCS1D01G175700 chr5A 92.135 89 4 3 202 289 486981991 486982077 4.780000e-24 122.0
32 TraesCS1D01G175700 chr5A 94.000 50 3 0 3478 3527 677167115 677167066 3.780000e-10 76.8
33 TraesCS1D01G175700 chr3A 91.209 91 7 1 200 289 109118270 109118360 4.780000e-24 122.0
34 TraesCS1D01G175700 chr4D 86.842 76 5 1 3452 3527 495988422 495988492 2.920000e-11 80.5
35 TraesCS1D01G175700 chr4D 86.765 68 4 2 3460 3527 495994478 495994416 1.760000e-08 71.3


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 TraesCS1D01G175700 chr1D 250068266 250071792 3526 True 6514.00 6514 100.000000 1 3527 1 chr1D.!!$R2 3526
1 TraesCS1D01G175700 chr1D 249754098 249755674 1576 True 1790.00 1790 87.334000 961 2521 1 chr1D.!!$R1 1560
2 TraesCS1D01G175700 chr1D 442798159 442799618 1459 False 1177.00 1177 81.652000 1079 2519 1 chr1D.!!$F3 1440
3 TraesCS1D01G175700 chr1D 389489295 389490741 1446 False 1090.00 1090 80.628000 1078 2515 1 chr1D.!!$F2 1437
4 TraesCS1D01G175700 chr1D 250137559 250139011 1452 True 1051.00 1051 80.287000 1087 2500 1 chr1D.!!$R3 1413
5 TraesCS1D01G175700 chr1B 364503346 364506803 3457 False 1344.00 3502 90.680667 137 2905 3 chr1B.!!$F2 2768
6 TraesCS1D01G175700 chr1B 522743330 522744770 1440 True 1122.00 1122 81.122000 1087 2515 1 chr1B.!!$R1 1428
7 TraesCS1D01G175700 chr1B 364423143 364424572 1429 False 1062.00 1062 80.598000 1092 2485 1 chr1B.!!$F1 1393
8 TraesCS1D01G175700 chr1B 364811158 364812753 1595 False 770.00 808 87.512000 960 2521 2 chr1B.!!$F3 1561
9 TraesCS1D01G175700 chr1A 319445963 319447542 1579 True 1781.00 1781 87.223000 961 2521 1 chr1A.!!$R1 1560
10 TraesCS1D01G175700 chr1A 319886699 319890708 4009 True 1210.75 3450 90.883750 1 3410 4 chr1A.!!$R3 3409
11 TraesCS1D01G175700 chr1A 488097689 488099138 1449 False 1083.00 1083 80.518000 1078 2515 1 chr1A.!!$F1 1437
12 TraesCS1D01G175700 chr1A 320154544 320155707 1163 True 861.00 861 80.736000 1378 2496 1 chr1A.!!$R2 1118

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
901 2011 0.948623 TCAACACGTTCCATCCGCTG 60.949 55.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2736 4092 0.037975 GTAACCGGCCTCTGAACGAA 60.038 55.0 0.0 0.0 0.0 3.85 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
33 34 6.323203 AGCATATGTCTATTTTCATGGCAC 57.677 37.500 4.29 0.00 32.35 5.01
45 46 3.144657 TCATGGCACTGAACAACTCAT 57.855 42.857 0.00 0.00 32.14 2.90
46 47 2.815503 TCATGGCACTGAACAACTCATG 59.184 45.455 0.00 0.00 32.14 3.07
50 51 2.880890 GGCACTGAACAACTCATGAACT 59.119 45.455 0.00 0.00 32.14 3.01
51 52 4.065088 GGCACTGAACAACTCATGAACTA 58.935 43.478 0.00 0.00 32.14 2.24
52 53 4.515191 GGCACTGAACAACTCATGAACTAA 59.485 41.667 0.00 0.00 32.14 2.24
53 54 5.444122 GCACTGAACAACTCATGAACTAAC 58.556 41.667 0.00 0.00 32.14 2.34
54 55 5.007626 GCACTGAACAACTCATGAACTAACA 59.992 40.000 0.00 0.00 32.14 2.41
55 56 6.422223 CACTGAACAACTCATGAACTAACAC 58.578 40.000 0.00 0.00 32.14 3.32
56 57 5.527582 ACTGAACAACTCATGAACTAACACC 59.472 40.000 0.00 0.00 32.14 4.16
57 58 5.432645 TGAACAACTCATGAACTAACACCA 58.567 37.500 0.00 0.00 0.00 4.17
58 59 5.883115 TGAACAACTCATGAACTAACACCAA 59.117 36.000 0.00 0.00 0.00 3.67
59 60 6.545666 TGAACAACTCATGAACTAACACCAAT 59.454 34.615 0.00 0.00 0.00 3.16
144 145 3.445805 GTCCTCTAGTGTTCCCTCTCTTG 59.554 52.174 0.00 0.00 0.00 3.02
163 164 4.750098 TCTTGCTACTTCCTTTCTTCAACG 59.250 41.667 0.00 0.00 0.00 4.10
243 245 2.110213 TTGGGTCACACTCGGCAC 59.890 61.111 0.00 0.00 0.00 5.01
244 246 2.736826 TTGGGTCACACTCGGCACA 61.737 57.895 0.00 0.00 0.00 4.57
312 1058 8.227507 ACTAGAGGCATAAAACCAATTATCCAT 58.772 33.333 0.00 0.00 0.00 3.41
313 1059 7.919385 AGAGGCATAAAACCAATTATCCATT 57.081 32.000 0.00 0.00 0.00 3.16
622 1723 1.402968 ACGCGAGCGATTTCCTTAGTA 59.597 47.619 24.72 0.00 42.83 1.82
623 1724 2.034305 ACGCGAGCGATTTCCTTAGTAT 59.966 45.455 24.72 0.00 42.83 2.12
624 1725 2.405357 CGCGAGCGATTTCCTTAGTATG 59.595 50.000 12.58 0.00 42.83 2.39
655 1756 5.182950 ACCGTTTCAAAGCATTGATATCACA 59.817 36.000 4.48 0.00 44.70 3.58
666 1767 9.715121 AAGCATTGATATCACACAAAGAAAAAT 57.285 25.926 4.48 0.00 0.00 1.82
901 2011 0.948623 TCAACACGTTCCATCCGCTG 60.949 55.000 0.00 0.00 0.00 5.18
947 2057 1.272203 ACACCGTCCTCATCTCAGTCT 60.272 52.381 0.00 0.00 0.00 3.24
1026 2142 1.296715 GTGGCACATCTTCCTCGGT 59.703 57.895 13.86 0.00 44.52 4.69
1332 2469 2.793160 CTTCGCTCAAGCTGCTGGGA 62.793 60.000 1.35 1.65 39.32 4.37
1648 2818 2.025155 TCTACAGGTCGAGGAAGATGC 58.975 52.381 0.00 0.00 0.00 3.91
1914 3108 0.969894 ACCTCTGTTCCGAGTTCCTG 59.030 55.000 0.00 0.00 0.00 3.86
2561 3914 4.125703 CTCCATCAGCCAGTAGTCAAATC 58.874 47.826 0.00 0.00 0.00 2.17
2568 3921 2.614481 GCCAGTAGTCAAATCCGACCAA 60.614 50.000 0.00 0.00 36.52 3.67
2685 4041 5.333798 CGCTTTCGAGAAATTGAGGTGTTTA 60.334 40.000 0.00 0.00 38.10 2.01
2686 4042 5.851703 GCTTTCGAGAAATTGAGGTGTTTAC 59.148 40.000 0.00 0.00 0.00 2.01
2699 4055 3.660865 GGTGTTTACCACTGTCTACTGG 58.339 50.000 0.00 0.00 46.71 4.00
2700 4056 3.070590 GGTGTTTACCACTGTCTACTGGT 59.929 47.826 0.00 0.00 46.71 4.00
2701 4057 4.443881 GGTGTTTACCACTGTCTACTGGTT 60.444 45.833 0.00 0.00 46.71 3.67
2702 4058 4.748600 GTGTTTACCACTGTCTACTGGTTC 59.251 45.833 0.00 0.00 41.28 3.62
2703 4059 3.928727 TTACCACTGTCTACTGGTTCG 57.071 47.619 0.00 0.00 41.28 3.95
2704 4060 1.700955 ACCACTGTCTACTGGTTCGT 58.299 50.000 0.00 0.00 37.51 3.85
2720 4076 1.411394 TCGTGCTGCGTGTTTACTAC 58.589 50.000 0.00 0.00 42.13 2.73
2721 4077 1.001048 TCGTGCTGCGTGTTTACTACT 60.001 47.619 0.00 0.00 42.13 2.57
2722 4078 1.385743 CGTGCTGCGTGTTTACTACTC 59.614 52.381 0.00 0.00 35.54 2.59
2723 4079 1.725164 GTGCTGCGTGTTTACTACTCC 59.275 52.381 0.00 0.00 0.00 3.85
2724 4080 1.341852 TGCTGCGTGTTTACTACTCCA 59.658 47.619 0.00 0.00 0.00 3.86
2736 4092 7.119846 GTGTTTACTACTCCAGCAATTGATTCT 59.880 37.037 10.34 0.00 0.00 2.40
2764 4384 4.038763 TCAGAGGCCGGTTACATATGTTAG 59.961 45.833 14.77 3.39 0.00 2.34
2866 4498 3.876300 GCTCGGAAAGCGTGACAT 58.124 55.556 0.00 0.00 42.21 3.06
2913 4546 2.402640 GTAGGCACGATAAGTCTCCG 57.597 55.000 0.00 0.00 0.00 4.63
2938 4571 4.168291 GAGGAAGGCGGGGCAGAG 62.168 72.222 0.00 0.00 0.00 3.35
2955 4588 3.551863 GCAGAGATATCTCCGGAGTGTTG 60.552 52.174 30.17 18.97 43.88 3.33
2962 4595 1.967779 TCTCCGGAGTGTTGATGACAA 59.032 47.619 30.17 4.05 40.65 3.18
2966 4599 2.993899 CCGGAGTGTTGATGACAAGTAC 59.006 50.000 0.00 0.00 40.65 2.73
2968 4601 3.921021 CGGAGTGTTGATGACAAGTACTC 59.079 47.826 0.00 13.75 43.21 2.59
2970 4603 5.140747 GAGTGTTGATGACAAGTACTCCT 57.859 43.478 0.00 0.00 40.97 3.69
2971 4604 6.268825 GAGTGTTGATGACAAGTACTCCTA 57.731 41.667 0.00 0.00 40.97 2.94
2972 4605 6.274157 AGTGTTGATGACAAGTACTCCTAG 57.726 41.667 0.00 0.00 40.65 3.02
2973 4606 5.775701 AGTGTTGATGACAAGTACTCCTAGT 59.224 40.000 0.00 0.00 40.65 2.57
2974 4607 6.267928 AGTGTTGATGACAAGTACTCCTAGTT 59.732 38.462 0.00 0.00 40.65 2.24
2976 4609 6.929049 TGTTGATGACAAGTACTCCTAGTTTG 59.071 38.462 0.00 0.00 36.64 2.93
2977 4610 6.665992 TGATGACAAGTACTCCTAGTTTGT 57.334 37.500 0.00 0.00 33.32 2.83
3017 4709 3.675225 CCTCCAATGCATATTACTCGTCG 59.325 47.826 0.00 0.00 0.00 5.12
3023 4715 6.292129 CAATGCATATTACTCGTCGTTCATC 58.708 40.000 0.00 0.00 0.00 2.92
3036 4728 4.551217 CGTCGTTCATCCGTTTGAGAAAAA 60.551 41.667 0.00 0.00 0.00 1.94
3042 4734 8.225107 CGTTCATCCGTTTGAGAAAAAGTAATA 58.775 33.333 0.00 0.00 0.00 0.98
3045 4737 8.673711 TCATCCGTTTGAGAAAAAGTAATATGG 58.326 33.333 0.00 0.00 0.00 2.74
3046 4738 7.989416 TCCGTTTGAGAAAAAGTAATATGGT 57.011 32.000 0.00 0.00 0.00 3.55
3047 4739 8.398878 TCCGTTTGAGAAAAAGTAATATGGTT 57.601 30.769 0.00 0.00 0.00 3.67
3048 4740 8.508875 TCCGTTTGAGAAAAAGTAATATGGTTC 58.491 33.333 0.00 0.00 0.00 3.62
3049 4741 7.480542 CCGTTTGAGAAAAAGTAATATGGTTCG 59.519 37.037 0.00 0.00 0.00 3.95
3050 4742 7.480542 CGTTTGAGAAAAAGTAATATGGTTCGG 59.519 37.037 0.00 0.00 0.00 4.30
3051 4743 6.995511 TGAGAAAAAGTAATATGGTTCGGG 57.004 37.500 0.00 0.00 0.00 5.14
3053 4745 6.821665 TGAGAAAAAGTAATATGGTTCGGGAG 59.178 38.462 0.00 0.00 0.00 4.30
3056 4748 3.339713 AGTAATATGGTTCGGGAGGGA 57.660 47.619 0.00 0.00 0.00 4.20
3057 4749 3.240302 AGTAATATGGTTCGGGAGGGAG 58.760 50.000 0.00 0.00 0.00 4.30
3058 4750 2.191981 AATATGGTTCGGGAGGGAGT 57.808 50.000 0.00 0.00 0.00 3.85
3059 4751 3.339713 AATATGGTTCGGGAGGGAGTA 57.660 47.619 0.00 0.00 0.00 2.59
3060 4752 3.562108 ATATGGTTCGGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
3061 4753 4.687262 ATATGGTTCGGGAGGGAGTATA 57.313 45.455 0.00 0.00 0.00 1.47
3062 4754 2.077687 TGGTTCGGGAGGGAGTATAC 57.922 55.000 0.00 0.00 0.00 1.47
3063 4755 1.288633 TGGTTCGGGAGGGAGTATACA 59.711 52.381 5.50 0.00 0.00 2.29
3064 4756 2.292389 TGGTTCGGGAGGGAGTATACAA 60.292 50.000 5.50 0.00 0.00 2.41
3065 4757 2.102084 GGTTCGGGAGGGAGTATACAAC 59.898 54.545 5.50 0.00 0.00 3.32
3066 4758 3.029570 GTTCGGGAGGGAGTATACAACT 58.970 50.000 5.50 0.00 42.80 3.16
3075 4767 2.910688 AGTATACAACTCCGGGCATG 57.089 50.000 0.00 0.00 30.33 4.06
3076 4768 2.116238 AGTATACAACTCCGGGCATGT 58.884 47.619 0.00 6.89 30.33 3.21
3077 4769 2.158957 AGTATACAACTCCGGGCATGTG 60.159 50.000 14.55 4.16 30.33 3.21
3078 4770 0.908910 ATACAACTCCGGGCATGTGA 59.091 50.000 14.55 3.07 0.00 3.58
3083 4775 0.620556 ACTCCGGGCATGTGAAGATT 59.379 50.000 0.00 0.00 0.00 2.40
3168 4861 2.910688 TGGGTGACTTCAGTTCTGAC 57.089 50.000 1.72 0.00 0.00 3.51
3203 4902 7.713507 ACGCTACTTTATTTGCATCCTGTATTA 59.286 33.333 0.00 0.00 0.00 0.98
3205 4904 9.273016 GCTACTTTATTTGCATCCTGTATTAGA 57.727 33.333 0.00 0.00 0.00 2.10
3214 4913 6.582636 TGCATCCTGTATTAGAGTTAACCTG 58.417 40.000 0.88 0.00 0.00 4.00
3222 4921 7.959175 TGTATTAGAGTTAACCTGAGTGTTGT 58.041 34.615 0.88 0.00 0.00 3.32
3225 4924 5.552870 AGAGTTAACCTGAGTGTTGTCAT 57.447 39.130 0.88 0.00 0.00 3.06
3227 4926 4.389374 AGTTAACCTGAGTGTTGTCATGG 58.611 43.478 0.88 0.00 0.00 3.66
3232 4931 2.810274 CCTGAGTGTTGTCATGGAAGTG 59.190 50.000 0.00 0.00 0.00 3.16
3238 4937 7.795047 TGAGTGTTGTCATGGAAGTGATATAT 58.205 34.615 0.00 0.00 0.00 0.86
3249 4948 7.712204 TGGAAGTGATATATATACTCCGCAA 57.288 36.000 0.00 0.00 0.00 4.85
3274 4973 1.420430 TCTTCTTCGTTGGACCCTGT 58.580 50.000 0.00 0.00 0.00 4.00
3290 4989 5.355350 GGACCCTGTGACTAGATTTCATTTG 59.645 44.000 0.00 0.00 0.00 2.32
3300 4999 7.719193 TGACTAGATTTCATTTGGTCAACTCAA 59.281 33.333 0.00 0.00 30.81 3.02
3339 5038 5.185828 AGACAACCAAAGGCATCTTAAATCC 59.814 40.000 0.00 0.00 32.01 3.01
3350 5049 7.036220 AGGCATCTTAAATCCGACTAATATCG 58.964 38.462 0.00 0.00 41.89 2.92
3367 5070 9.444600 ACTAATATCGAAGAAAACAAAGGCTAA 57.555 29.630 0.00 0.00 43.58 3.09
3368 5071 9.704098 CTAATATCGAAGAAAACAAAGGCTAAC 57.296 33.333 0.00 0.00 43.58 2.34
3370 5073 5.164606 TCGAAGAAAACAAAGGCTAACAC 57.835 39.130 0.00 0.00 0.00 3.32
3386 5089 2.479566 ACACCATGGCTAGACAACAG 57.520 50.000 13.04 0.00 0.00 3.16
3392 5095 1.913778 TGGCTAGACAACAGGACGTA 58.086 50.000 0.00 0.00 0.00 3.57
3399 5102 3.714391 AGACAACAGGACGTAGAACAAC 58.286 45.455 0.00 0.00 0.00 3.32
3401 5104 3.192466 ACAACAGGACGTAGAACAACAC 58.808 45.455 0.00 0.00 0.00 3.32
3434 5137 8.730093 AAAGTAAAATTACATTAAGGGTGGGT 57.270 30.769 6.13 0.00 36.12 4.51
3435 5138 8.730093 AAGTAAAATTACATTAAGGGTGGGTT 57.270 30.769 6.13 0.00 36.12 4.11
3436 5139 8.730093 AGTAAAATTACATTAAGGGTGGGTTT 57.270 30.769 6.13 0.00 36.12 3.27
3437 5140 8.590204 AGTAAAATTACATTAAGGGTGGGTTTG 58.410 33.333 6.13 0.00 36.12 2.93
3438 5141 6.367374 AAATTACATTAAGGGTGGGTTTGG 57.633 37.500 0.00 0.00 0.00 3.28
3439 5142 4.472690 TTACATTAAGGGTGGGTTTGGT 57.527 40.909 0.00 0.00 0.00 3.67
3440 5143 3.338110 ACATTAAGGGTGGGTTTGGTT 57.662 42.857 0.00 0.00 0.00 3.67
3441 5144 2.969262 ACATTAAGGGTGGGTTTGGTTG 59.031 45.455 0.00 0.00 0.00 3.77
3442 5145 1.415200 TTAAGGGTGGGTTTGGTTGC 58.585 50.000 0.00 0.00 0.00 4.17
3443 5146 0.261991 TAAGGGTGGGTTTGGTTGCA 59.738 50.000 0.00 0.00 0.00 4.08
3444 5147 0.618968 AAGGGTGGGTTTGGTTGCAA 60.619 50.000 0.00 0.00 0.00 4.08
3445 5148 0.618968 AGGGTGGGTTTGGTTGCAAA 60.619 50.000 0.00 0.00 0.00 3.68
3446 5149 0.179059 GGGTGGGTTTGGTTGCAAAG 60.179 55.000 0.00 0.00 0.00 2.77
3447 5150 0.539518 GGTGGGTTTGGTTGCAAAGT 59.460 50.000 0.00 0.00 0.00 2.66
3448 5151 1.757699 GGTGGGTTTGGTTGCAAAGTA 59.242 47.619 0.00 0.00 0.00 2.24
3449 5152 2.367241 GGTGGGTTTGGTTGCAAAGTAT 59.633 45.455 0.00 0.00 0.00 2.12
3450 5153 3.181459 GGTGGGTTTGGTTGCAAAGTATT 60.181 43.478 0.00 0.00 0.00 1.89
3451 5154 4.447290 GTGGGTTTGGTTGCAAAGTATTT 58.553 39.130 0.00 0.00 40.26 1.40
3452 5155 4.878971 GTGGGTTTGGTTGCAAAGTATTTT 59.121 37.500 0.00 0.00 35.03 1.82
3453 5156 5.007234 GTGGGTTTGGTTGCAAAGTATTTTC 59.993 40.000 0.00 0.00 35.03 2.29
3454 5157 5.119694 GGGTTTGGTTGCAAAGTATTTTCA 58.880 37.500 0.00 0.00 35.03 2.69
3455 5158 5.586643 GGGTTTGGTTGCAAAGTATTTTCAA 59.413 36.000 0.00 0.00 38.82 2.69
3456 5159 6.094186 GGGTTTGGTTGCAAAGTATTTTCAAA 59.906 34.615 0.00 0.26 42.43 2.69
3457 5160 7.186128 GGTTTGGTTGCAAAGTATTTTCAAAG 58.814 34.615 0.00 0.00 42.43 2.77
3458 5161 7.148323 GGTTTGGTTGCAAAGTATTTTCAAAGT 60.148 33.333 0.00 0.00 42.43 2.66
3459 5162 8.874816 GTTTGGTTGCAAAGTATTTTCAAAGTA 58.125 29.630 0.00 0.00 42.43 2.24
3460 5163 9.606631 TTTGGTTGCAAAGTATTTTCAAAGTAT 57.393 25.926 0.00 0.00 42.43 2.12
3461 5164 9.606631 TTGGTTGCAAAGTATTTTCAAAGTATT 57.393 25.926 0.00 0.00 42.43 1.89
3462 5165 9.606631 TGGTTGCAAAGTATTTTCAAAGTATTT 57.393 25.926 0.00 0.00 42.43 1.40
3477 5180 8.918202 TCAAAGTATTTCAAGAATACCACAGT 57.082 30.769 5.54 0.00 35.03 3.55
3495 5198 8.245195 ACCACAGTATTTTGAAAAACTATGGT 57.755 30.769 20.15 20.15 0.00 3.55
3496 5199 8.700973 ACCACAGTATTTTGAAAAACTATGGTT 58.299 29.630 20.15 11.21 37.24 3.67
3497 5200 9.541143 CCACAGTATTTTGAAAAACTATGGTTT 57.459 29.630 15.69 0.65 46.27 3.27
3522 5225 6.715347 AAATACTTTGAAGTGTTTGGCTCT 57.285 33.333 15.00 0.00 44.94 4.09
3523 5226 7.817418 AAATACTTTGAAGTGTTTGGCTCTA 57.183 32.000 15.00 0.00 44.94 2.43
3524 5227 7.440523 AATACTTTGAAGTGTTTGGCTCTAG 57.559 36.000 6.64 0.00 37.08 2.43
3525 5228 4.781934 ACTTTGAAGTGTTTGGCTCTAGT 58.218 39.130 0.00 0.00 37.98 2.57
3526 5229 5.193679 ACTTTGAAGTGTTTGGCTCTAGTT 58.806 37.500 0.00 0.00 37.98 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.016860 TCAGTGCCATGAAAATAGACATATGC 60.017 38.462 1.58 0.00 0.00 3.14
12 13 7.500720 TCAGTGCCATGAAAATAGACATATG 57.499 36.000 0.00 0.00 0.00 1.78
33 34 5.527214 TGGTGTTAGTTCATGAGTTGTTCAG 59.473 40.000 0.00 0.00 39.68 3.02
54 55 3.283751 TGTTTGGTTCTTCACGATTGGT 58.716 40.909 0.00 0.00 0.00 3.67
55 56 3.980646 TGTTTGGTTCTTCACGATTGG 57.019 42.857 0.00 0.00 0.00 3.16
56 57 4.667262 TGTTGTTTGGTTCTTCACGATTG 58.333 39.130 0.00 0.00 0.00 2.67
57 58 4.974368 TGTTGTTTGGTTCTTCACGATT 57.026 36.364 0.00 0.00 0.00 3.34
58 59 4.156922 TGTTGTTGTTTGGTTCTTCACGAT 59.843 37.500 0.00 0.00 0.00 3.73
59 60 3.502595 TGTTGTTGTTTGGTTCTTCACGA 59.497 39.130 0.00 0.00 0.00 4.35
144 145 4.083961 GGAACGTTGAAGAAAGGAAGTAGC 60.084 45.833 5.00 0.00 0.00 3.58
163 164 1.134371 GGAGGAGGCATGTGTAGGAAC 60.134 57.143 0.00 0.00 0.00 3.62
243 245 6.859508 GTGTTTTCGAAAACTAGGGGTAAATG 59.140 38.462 38.87 0.00 46.37 2.32
244 246 6.774170 AGTGTTTTCGAAAACTAGGGGTAAAT 59.226 34.615 38.87 21.78 46.37 1.40
437 1206 5.118990 TCTAGCTGTCAATTAATGAGCACC 58.881 41.667 0.00 0.00 39.19 5.01
622 1723 2.223947 GCTTTGAAACGGTTTCCCACAT 60.224 45.455 25.99 0.00 38.90 3.21
623 1724 1.135333 GCTTTGAAACGGTTTCCCACA 59.865 47.619 25.99 9.42 38.90 4.17
624 1725 1.135333 TGCTTTGAAACGGTTTCCCAC 59.865 47.619 25.99 15.38 38.90 4.61
634 1735 7.872163 TTGTGTGATATCAATGCTTTGAAAC 57.128 32.000 17.82 13.72 44.70 2.78
709 1818 5.726397 TCCCTCTTCGATTTTTAATCGTGA 58.274 37.500 18.03 15.80 41.77 4.35
947 2057 0.749091 CTGCTGGAATGGATGCGGAA 60.749 55.000 0.00 0.00 34.02 4.30
1026 2142 0.389391 GGATGGCGAAGAGGATCGAA 59.611 55.000 0.24 0.00 45.48 3.71
1332 2469 2.872245 CGTGATGGTGTTGTTGTTCTCT 59.128 45.455 0.00 0.00 0.00 3.10
1648 2818 0.182299 GGCAGGAAGGAGAAGATGGG 59.818 60.000 0.00 0.00 0.00 4.00
2148 3495 1.153168 CCCGCCGATTTCCATGTCT 60.153 57.895 0.00 0.00 0.00 3.41
2292 3645 1.599518 GTTGCCGGTCACATCCACA 60.600 57.895 1.90 0.00 0.00 4.17
2561 3914 1.486211 AGGAGTGGACTATTGGTCGG 58.514 55.000 0.00 0.00 45.35 4.79
2568 3921 2.814919 CGAAGCGATAGGAGTGGACTAT 59.185 50.000 0.00 0.00 34.00 2.12
2687 4043 1.000163 AGCACGAACCAGTAGACAGTG 60.000 52.381 0.00 0.00 0.00 3.66
2689 4045 1.702886 CAGCACGAACCAGTAGACAG 58.297 55.000 0.00 0.00 0.00 3.51
2690 4046 0.319555 GCAGCACGAACCAGTAGACA 60.320 55.000 0.00 0.00 0.00 3.41
2691 4047 2.446341 GCAGCACGAACCAGTAGAC 58.554 57.895 0.00 0.00 0.00 2.59
2692 4048 4.988065 GCAGCACGAACCAGTAGA 57.012 55.556 0.00 0.00 0.00 2.59
2703 4059 1.725164 GGAGTAGTAAACACGCAGCAC 59.275 52.381 0.00 0.00 0.00 4.40
2704 4060 1.341852 TGGAGTAGTAAACACGCAGCA 59.658 47.619 0.00 0.00 0.00 4.41
2720 4076 4.154737 TGAACGAAGAATCAATTGCTGGAG 59.845 41.667 0.00 0.00 0.00 3.86
2721 4077 4.071423 TGAACGAAGAATCAATTGCTGGA 58.929 39.130 0.00 0.00 0.00 3.86
2722 4078 4.154737 TCTGAACGAAGAATCAATTGCTGG 59.845 41.667 0.00 0.00 0.00 4.85
2723 4079 5.287170 TCTGAACGAAGAATCAATTGCTG 57.713 39.130 0.00 0.00 0.00 4.41
2724 4080 4.394300 CCTCTGAACGAAGAATCAATTGCT 59.606 41.667 0.00 0.00 0.00 3.91
2736 4092 0.037975 GTAACCGGCCTCTGAACGAA 60.038 55.000 0.00 0.00 0.00 3.85
2764 4384 2.030540 TGCTCTTGCTTGCTCAATCAAC 60.031 45.455 0.00 0.00 40.48 3.18
2866 4498 0.979709 CCTCCTGCCTCATCCACTCA 60.980 60.000 0.00 0.00 0.00 3.41
2911 4544 0.179124 CGCCTTCCTCTCTTTCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
2913 4546 0.176910 CCCGCCTTCCTCTCTTTCTC 59.823 60.000 0.00 0.00 0.00 2.87
2938 4571 4.038042 TGTCATCAACACTCCGGAGATATC 59.962 45.833 37.69 15.45 31.20 1.63
2955 4588 9.485206 TTTAACAAACTAGGAGTACTTGTCATC 57.515 33.333 0.00 0.00 30.39 2.92
2996 4688 4.299155 ACGACGAGTAATATGCATTGGAG 58.701 43.478 3.54 0.00 0.00 3.86
2999 4691 5.635549 TGAACGACGAGTAATATGCATTG 57.364 39.130 3.54 0.00 0.00 2.82
3023 4715 7.480542 CGAACCATATTACTTTTTCTCAAACGG 59.519 37.037 0.00 0.00 0.00 4.44
3036 4728 3.240302 CTCCCTCCCGAACCATATTACT 58.760 50.000 0.00 0.00 0.00 2.24
3042 4734 2.090943 TGTATACTCCCTCCCGAACCAT 60.091 50.000 4.17 0.00 0.00 3.55
3043 4735 1.288633 TGTATACTCCCTCCCGAACCA 59.711 52.381 4.17 0.00 0.00 3.67
3044 4736 2.077687 TGTATACTCCCTCCCGAACC 57.922 55.000 4.17 0.00 0.00 3.62
3045 4737 3.029570 AGTTGTATACTCCCTCCCGAAC 58.970 50.000 4.17 0.00 28.23 3.95
3046 4738 3.294214 GAGTTGTATACTCCCTCCCGAA 58.706 50.000 4.17 0.00 46.30 4.30
3047 4739 2.941480 GAGTTGTATACTCCCTCCCGA 58.059 52.381 4.17 0.00 46.30 5.14
3056 4748 2.116238 ACATGCCCGGAGTTGTATACT 58.884 47.619 0.73 0.00 40.71 2.12
3057 4749 2.159014 TCACATGCCCGGAGTTGTATAC 60.159 50.000 0.73 0.00 0.00 1.47
3058 4750 2.112190 TCACATGCCCGGAGTTGTATA 58.888 47.619 0.73 0.00 0.00 1.47
3059 4751 0.908910 TCACATGCCCGGAGTTGTAT 59.091 50.000 0.73 0.00 0.00 2.29
3060 4752 0.687920 TTCACATGCCCGGAGTTGTA 59.312 50.000 0.73 0.00 0.00 2.41
3061 4753 0.606401 CTTCACATGCCCGGAGTTGT 60.606 55.000 0.73 0.00 0.00 3.32
3062 4754 0.321564 TCTTCACATGCCCGGAGTTG 60.322 55.000 0.73 0.00 0.00 3.16
3063 4755 0.620556 ATCTTCACATGCCCGGAGTT 59.379 50.000 0.73 0.00 0.00 3.01
3064 4756 0.620556 AATCTTCACATGCCCGGAGT 59.379 50.000 0.73 0.00 0.00 3.85
3065 4757 1.755179 AAATCTTCACATGCCCGGAG 58.245 50.000 0.73 0.00 0.00 4.63
3066 4758 2.214376 AAAATCTTCACATGCCCGGA 57.786 45.000 0.73 0.00 0.00 5.14
3096 4788 8.882415 TCTTGGACGGATACATCTATTTTAAC 57.118 34.615 0.00 0.00 0.00 2.01
3099 4791 9.490379 GTTATCTTGGACGGATACATCTATTTT 57.510 33.333 0.00 0.00 0.00 1.82
3102 4794 8.423906 AAGTTATCTTGGACGGATACATCTAT 57.576 34.615 0.00 0.00 32.09 1.98
3103 4795 7.834881 AAGTTATCTTGGACGGATACATCTA 57.165 36.000 0.00 0.00 32.09 1.98
3104 4796 6.732896 AAGTTATCTTGGACGGATACATCT 57.267 37.500 0.00 0.00 32.09 2.90
3105 4797 6.761714 ACAAAGTTATCTTGGACGGATACATC 59.238 38.462 0.00 0.00 33.79 3.06
3106 4798 6.650120 ACAAAGTTATCTTGGACGGATACAT 58.350 36.000 0.00 0.00 33.79 2.29
3107 4799 6.045072 ACAAAGTTATCTTGGACGGATACA 57.955 37.500 0.00 0.00 33.79 2.29
3108 4800 6.980051 AACAAAGTTATCTTGGACGGATAC 57.020 37.500 0.00 0.00 33.79 2.24
3168 4861 7.735500 TGCAAATAAAGTAGCGTTAACACTAG 58.264 34.615 6.39 0.00 0.00 2.57
3203 4902 5.300752 CATGACAACACTCAGGTTAACTCT 58.699 41.667 5.42 0.00 0.00 3.24
3205 4904 4.102524 TCCATGACAACACTCAGGTTAACT 59.897 41.667 5.42 0.00 0.00 2.24
3214 4913 9.935241 ATATATATCACTTCCATGACAACACTC 57.065 33.333 0.00 0.00 0.00 3.51
3222 4921 7.559897 TGCGGAGTATATATATCACTTCCATGA 59.440 37.037 0.00 0.00 0.00 3.07
3225 4924 7.712204 TTGCGGAGTATATATATCACTTCCA 57.288 36.000 0.00 0.24 0.00 3.53
3227 4926 9.803315 TCATTTGCGGAGTATATATATCACTTC 57.197 33.333 0.00 0.59 0.00 3.01
3238 4937 6.420903 CGAAGAAGATTCATTTGCGGAGTATA 59.579 38.462 0.00 0.00 0.00 1.47
3242 4941 3.372206 ACGAAGAAGATTCATTTGCGGAG 59.628 43.478 0.00 0.00 0.00 4.63
3249 4948 4.010349 GGGTCCAACGAAGAAGATTCATT 58.990 43.478 0.00 0.00 0.00 2.57
3274 4973 7.223584 TGAGTTGACCAAATGAAATCTAGTCA 58.776 34.615 0.00 0.00 0.00 3.41
3306 5005 8.646900 AGATGCCTTTGGTTGTCTTTATTAAAA 58.353 29.630 0.00 0.00 0.00 1.52
3307 5006 8.189119 AGATGCCTTTGGTTGTCTTTATTAAA 57.811 30.769 0.00 0.00 0.00 1.52
3308 5007 7.775053 AGATGCCTTTGGTTGTCTTTATTAA 57.225 32.000 0.00 0.00 0.00 1.40
3312 5011 7.589958 TTTAAGATGCCTTTGGTTGTCTTTA 57.410 32.000 0.00 0.00 33.94 1.85
3313 5012 6.478512 TTTAAGATGCCTTTGGTTGTCTTT 57.521 33.333 0.00 0.00 33.94 2.52
3315 5014 5.185828 GGATTTAAGATGCCTTTGGTTGTCT 59.814 40.000 0.00 0.00 33.94 3.41
3316 5015 5.410924 GGATTTAAGATGCCTTTGGTTGTC 58.589 41.667 0.00 0.00 33.94 3.18
3317 5016 4.082245 CGGATTTAAGATGCCTTTGGTTGT 60.082 41.667 0.00 0.00 33.94 3.32
3318 5017 4.157656 TCGGATTTAAGATGCCTTTGGTTG 59.842 41.667 0.00 0.00 33.94 3.77
3319 5018 4.157840 GTCGGATTTAAGATGCCTTTGGTT 59.842 41.667 0.00 0.00 33.94 3.67
3327 5026 8.462143 TTCGATATTAGTCGGATTTAAGATGC 57.538 34.615 0.00 0.00 41.74 3.91
3339 5038 6.900299 GCCTTTGTTTTCTTCGATATTAGTCG 59.100 38.462 0.00 0.00 42.74 4.18
3350 5049 5.257082 TGGTGTTAGCCTTTGTTTTCTTC 57.743 39.130 0.00 0.00 0.00 2.87
3367 5070 1.003580 CCTGTTGTCTAGCCATGGTGT 59.996 52.381 14.67 3.61 0.00 4.16
3368 5071 1.278985 TCCTGTTGTCTAGCCATGGTG 59.721 52.381 14.67 4.40 0.00 4.17
3370 5073 1.740380 CGTCCTGTTGTCTAGCCATGG 60.740 57.143 7.63 7.63 0.00 3.66
3409 5112 8.730093 ACCCACCCTTAATGTAATTTTACTTT 57.270 30.769 2.45 4.86 37.87 2.66
3410 5113 8.730093 AACCCACCCTTAATGTAATTTTACTT 57.270 30.769 2.45 0.00 37.87 2.24
3411 5114 8.590204 CAAACCCACCCTTAATGTAATTTTACT 58.410 33.333 2.45 0.00 37.87 2.24
3412 5115 7.820386 CCAAACCCACCCTTAATGTAATTTTAC 59.180 37.037 0.00 0.00 37.87 2.01
3413 5116 7.513091 ACCAAACCCACCCTTAATGTAATTTTA 59.487 33.333 0.00 0.00 37.87 1.52
3414 5117 6.330514 ACCAAACCCACCCTTAATGTAATTTT 59.669 34.615 0.00 0.00 37.87 1.82
3415 5118 5.847265 ACCAAACCCACCCTTAATGTAATTT 59.153 36.000 0.00 0.00 37.87 1.82
3416 5119 5.407936 ACCAAACCCACCCTTAATGTAATT 58.592 37.500 0.00 0.00 41.28 1.40
3417 5120 5.018374 ACCAAACCCACCCTTAATGTAAT 57.982 39.130 0.00 0.00 0.00 1.89
3418 5121 4.472690 ACCAAACCCACCCTTAATGTAA 57.527 40.909 0.00 0.00 0.00 2.41
3419 5122 4.153411 CAACCAAACCCACCCTTAATGTA 58.847 43.478 0.00 0.00 0.00 2.29
3420 5123 2.969262 CAACCAAACCCACCCTTAATGT 59.031 45.455 0.00 0.00 0.00 2.71
3421 5124 2.289382 GCAACCAAACCCACCCTTAATG 60.289 50.000 0.00 0.00 0.00 1.90
3422 5125 1.974957 GCAACCAAACCCACCCTTAAT 59.025 47.619 0.00 0.00 0.00 1.40
3423 5126 1.343075 TGCAACCAAACCCACCCTTAA 60.343 47.619 0.00 0.00 0.00 1.85
3424 5127 0.261991 TGCAACCAAACCCACCCTTA 59.738 50.000 0.00 0.00 0.00 2.69
3425 5128 0.618968 TTGCAACCAAACCCACCCTT 60.619 50.000 0.00 0.00 0.00 3.95
3426 5129 0.618968 TTTGCAACCAAACCCACCCT 60.619 50.000 0.00 0.00 36.09 4.34
3427 5130 0.179059 CTTTGCAACCAAACCCACCC 60.179 55.000 0.00 0.00 36.09 4.61
3428 5131 0.539518 ACTTTGCAACCAAACCCACC 59.460 50.000 0.00 0.00 36.09 4.61
3429 5132 3.744238 ATACTTTGCAACCAAACCCAC 57.256 42.857 0.00 0.00 36.09 4.61
3430 5133 4.762289 AAATACTTTGCAACCAAACCCA 57.238 36.364 0.00 0.00 36.09 4.51
3431 5134 5.119694 TGAAAATACTTTGCAACCAAACCC 58.880 37.500 0.00 0.00 36.09 4.11
3432 5135 6.670077 TTGAAAATACTTTGCAACCAAACC 57.330 33.333 0.00 0.00 36.09 3.27
3433 5136 7.747888 ACTTTGAAAATACTTTGCAACCAAAC 58.252 30.769 0.00 0.00 36.09 2.93
3434 5137 7.913674 ACTTTGAAAATACTTTGCAACCAAA 57.086 28.000 0.00 0.00 38.56 3.28
3435 5138 9.606631 AATACTTTGAAAATACTTTGCAACCAA 57.393 25.926 0.00 0.00 0.00 3.67
3436 5139 9.606631 AAATACTTTGAAAATACTTTGCAACCA 57.393 25.926 0.00 0.00 0.00 3.67
3451 5154 9.349713 ACTGTGGTATTCTTGAAATACTTTGAA 57.650 29.630 7.60 0.00 34.44 2.69
3452 5155 8.918202 ACTGTGGTATTCTTGAAATACTTTGA 57.082 30.769 7.60 0.00 34.44 2.69
3499 5202 6.715347 AGAGCCAAACACTTCAAAGTATTT 57.285 33.333 0.00 0.00 36.16 1.40
3500 5203 6.998673 ACTAGAGCCAAACACTTCAAAGTATT 59.001 34.615 0.00 0.00 37.08 1.89
3501 5204 6.534634 ACTAGAGCCAAACACTTCAAAGTAT 58.465 36.000 0.00 0.00 37.08 2.12
3502 5205 5.925509 ACTAGAGCCAAACACTTCAAAGTA 58.074 37.500 0.00 0.00 37.08 2.24
3503 5206 4.781934 ACTAGAGCCAAACACTTCAAAGT 58.218 39.130 0.00 0.00 40.60 2.66
3504 5207 5.757850 AACTAGAGCCAAACACTTCAAAG 57.242 39.130 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.