Multiple sequence alignment - TraesCS3B01G426100

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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 TraesCS3B01G426100 chr3B 100.000 5596 0 0 1 5596 664116510 664110915 0.000000e+00 10334.0
1 TraesCS3B01G426100 chr3B 89.864 513 51 1 1 512 770113769 770113257 0.000000e+00 658.0
2 TraesCS3B01G426100 chr3D 95.326 3038 101 22 2589 5596 502963166 502960140 0.000000e+00 4785.0
3 TraesCS3B01G426100 chr3D 90.274 1676 73 28 871 2507 502964789 502963165 0.000000e+00 2109.0
4 TraesCS3B01G426100 chr3D 90.672 536 43 6 1 535 502965954 502965425 0.000000e+00 706.0
5 TraesCS3B01G426100 chr3D 90.253 513 49 1 1 512 20400784 20401296 0.000000e+00 669.0
6 TraesCS3B01G426100 chr3D 95.399 326 13 2 520 845 502965340 502965017 8.310000e-143 518.0
7 TraesCS3B01G426100 chr3A 92.996 3041 153 31 2589 5596 641828031 641825018 0.000000e+00 4381.0
8 TraesCS3B01G426100 chr3A 93.662 1625 85 4 893 2507 641829646 641828030 0.000000e+00 2414.0
9 TraesCS3B01G426100 chr3A 89.844 512 51 1 1 511 722502030 722501519 0.000000e+00 656.0
10 TraesCS3B01G426100 chr3A 96.875 32 0 1 4583 4614 597829787 597829817 1.000000e-02 52.8
11 TraesCS3B01G426100 chr7D 90.114 526 48 4 1 525 607214933 607214411 0.000000e+00 680.0
12 TraesCS3B01G426100 chr4A 90.570 509 46 2 1 508 698370188 698370695 0.000000e+00 673.0
13 TraesCS3B01G426100 chr4A 96.875 32 0 1 4583 4614 174387615 174387645 1.000000e-02 52.8
14 TraesCS3B01G426100 chr4A 96.875 32 0 1 4583 4614 603658317 603658287 1.000000e-02 52.8
15 TraesCS3B01G426100 chr2D 90.020 511 49 2 3 512 277675888 277675379 0.000000e+00 660.0
16 TraesCS3B01G426100 chr2D 97.248 109 3 0 3291 3399 630722593 630722485 9.570000e-43 185.0
17 TraesCS3B01G426100 chr1D 89.689 514 50 3 1 512 235663922 235664434 0.000000e+00 652.0
18 TraesCS3B01G426100 chr1D 96.330 109 4 0 3291 3399 470825917 470826025 4.450000e-41 180.0
19 TraesCS3B01G426100 chr1B 89.443 521 49 4 1 517 169693093 169692575 0.000000e+00 652.0
20 TraesCS3B01G426100 chr6B 79.646 339 55 12 503 835 688626372 688626042 1.210000e-56 231.0
21 TraesCS3B01G426100 chr1A 98.864 88 1 0 2506 2593 108815275 108815188 2.090000e-34 158.0
22 TraesCS3B01G426100 chr1A 93.137 102 7 0 3298 3399 58344885 58344986 3.490000e-32 150.0
23 TraesCS3B01G426100 chr6D 96.774 93 1 2 2498 2590 68082855 68082945 2.700000e-33 154.0
24 TraesCS3B01G426100 chr2A 95.789 95 4 0 2503 2597 78805674 78805768 2.700000e-33 154.0
25 TraesCS3B01G426100 chrUn 95.745 94 4 0 2504 2597 316200537 316200630 9.710000e-33 152.0
26 TraesCS3B01G426100 chrUn 94.792 96 5 0 3304 3399 43011311 43011216 3.490000e-32 150.0
27 TraesCS3B01G426100 chrUn 93.137 102 7 0 3298 3399 43185083 43185184 3.490000e-32 150.0
28 TraesCS3B01G426100 chrUn 93.137 102 7 0 3298 3399 394795495 394795596 3.490000e-32 150.0
29 TraesCS3B01G426100 chrUn 94.792 96 5 0 3304 3399 431281541 431281446 3.490000e-32 150.0
30 TraesCS3B01G426100 chr6A 95.745 94 4 0 2504 2597 266828675 266828768 9.710000e-33 152.0
31 TraesCS3B01G426100 chr6A 95.745 94 4 0 2504 2597 266868292 266868385 9.710000e-33 152.0
32 TraesCS3B01G426100 chr5D 96.703 91 3 0 2500 2590 210057888 210057978 9.710000e-33 152.0
33 TraesCS3B01G426100 chr2B 90.826 109 5 3 2484 2590 583156215 583156320 2.100000e-29 141.0
34 TraesCS3B01G426100 chr2B 90.654 107 7 3 2493 2598 232350874 232350978 7.560000e-29 139.0
35 TraesCS3B01G426100 chr7A 96.875 32 0 1 4583 4614 566028968 566028998 1.000000e-02 52.8


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 TraesCS3B01G426100 chr3B 664110915 664116510 5595 True 10334.0 10334 100.00000 1 5596 1 chr3B.!!$R1 5595
1 TraesCS3B01G426100 chr3B 770113257 770113769 512 True 658.0 658 89.86400 1 512 1 chr3B.!!$R2 511
2 TraesCS3B01G426100 chr3D 502960140 502965954 5814 True 2029.5 4785 92.91775 1 5596 4 chr3D.!!$R1 5595
3 TraesCS3B01G426100 chr3D 20400784 20401296 512 False 669.0 669 90.25300 1 512 1 chr3D.!!$F1 511
4 TraesCS3B01G426100 chr3A 641825018 641829646 4628 True 3397.5 4381 93.32900 893 5596 2 chr3A.!!$R2 4703
5 TraesCS3B01G426100 chr3A 722501519 722502030 511 True 656.0 656 89.84400 1 511 1 chr3A.!!$R1 510
6 TraesCS3B01G426100 chr7D 607214411 607214933 522 True 680.0 680 90.11400 1 525 1 chr7D.!!$R1 524
7 TraesCS3B01G426100 chr4A 698370188 698370695 507 False 673.0 673 90.57000 1 508 1 chr4A.!!$F2 507
8 TraesCS3B01G426100 chr2D 277675379 277675888 509 True 660.0 660 90.02000 3 512 1 chr2D.!!$R1 509
9 TraesCS3B01G426100 chr1D 235663922 235664434 512 False 652.0 652 89.68900 1 512 1 chr1D.!!$F1 511
10 TraesCS3B01G426100 chr1B 169692575 169693093 518 True 652.0 652 89.44300 1 517 1 chr1B.!!$R1 516

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
188 192 0.944386 GTTGCTTTGAAGTCGGAGCA 59.056 50.0 4.79 4.79 42.84 4.26 F
1302 1625 0.101939 CGAAGTCGCCCCTTAGTACC 59.898 60.0 0.00 0.00 0.00 3.34 F
1503 1841 0.249955 CACCCCCAACATTGCCATTC 59.750 55.0 0.00 0.00 0.00 2.67 F
1760 2100 0.387367 ATCGCTGCATACGTCGATCC 60.387 55.0 0.00 0.00 37.09 3.36 F
2762 3113 0.323957 ACACGCCTCCTTACCCTTTC 59.676 55.0 0.00 0.00 0.00 2.62 F
4282 4636 0.178998 CTTGCCCAGGCTATGCTGAT 60.179 55.0 10.58 0.00 42.51 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1841 0.029300 CAACACACACGAAAGGCTGG 59.971 55.000 0.00 0.00 0.00 4.85 R
2595 2945 0.249120 CAGACTGGGTGCCGAACATA 59.751 55.000 0.00 0.00 0.00 2.29 R
2598 2948 0.249398 ATACAGACTGGGTGCCGAAC 59.751 55.000 7.51 0.00 0.00 3.95 R
2894 3245 1.599071 CGATTGTCGCAGCCAACATAT 59.401 47.619 0.00 0.00 31.14 1.78 R
4509 4863 1.002430 TCTCACCATGTCAGGTTCTGC 59.998 52.381 0.00 0.00 40.77 4.26 R
5444 5831 0.528466 CGATCGCCAGCTGAGCTTAA 60.528 55.000 17.39 5.85 36.40 1.85 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
45 46 3.645975 CTTCGCCGCGTGGTTTGT 61.646 61.111 17.91 0.00 37.67 2.83
56 60 2.114411 GGTTTGTTGAGGCGGGGA 59.886 61.111 0.00 0.00 0.00 4.81
188 192 0.944386 GTTGCTTTGAAGTCGGAGCA 59.056 50.000 4.79 4.79 42.84 4.26
189 193 3.395210 TGCTTTGAAGTCGGAGCAA 57.605 47.368 6.09 0.00 41.72 3.91
200 204 3.423154 GGAGCAACGTTGGAGCGG 61.423 66.667 28.33 3.46 35.98 5.52
242 246 2.358247 ATTCGGTGGTCGTGTGCC 60.358 61.111 0.00 0.00 40.32 5.01
243 247 3.894547 ATTCGGTGGTCGTGTGCCC 62.895 63.158 0.00 0.00 40.32 5.36
258 262 2.745698 CCCTCTGCACAGTCAGCA 59.254 61.111 0.00 0.00 40.19 4.41
277 281 4.157289 CAGCACAAGTCCTGCATATTTTCT 59.843 41.667 0.00 0.00 37.08 2.52
406 410 1.001020 GGTGCCCATGTCATGTGGA 60.001 57.895 19.09 5.14 39.12 4.02
426 431 5.410439 GTGGATTGTGTTGTATCGGTTTAGT 59.590 40.000 0.00 0.00 0.00 2.24
446 451 7.989416 TTAGTCTGGTTTTCCGTCAATTAAT 57.011 32.000 0.00 0.00 44.36 1.40
451 456 5.074115 TGGTTTTCCGTCAATTAATCAGGT 58.926 37.500 0.00 0.00 44.36 4.00
462 467 8.552034 CGTCAATTAATCAGGTAATTCTCTTCC 58.448 37.037 0.00 0.00 32.53 3.46
483 488 4.094294 TCCTCTTAATCAACGAAAATGGCG 59.906 41.667 0.00 0.00 0.00 5.69
612 711 1.834822 ATGCTCGGTCTCTAGGCCC 60.835 63.158 0.00 0.00 0.00 5.80
631 730 2.454941 GGACTGGGAGGAGGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
723 822 4.479993 GCCGGACTGCTGCTGGAT 62.480 66.667 5.05 0.00 33.45 3.41
854 975 1.079438 GGGGACTGGTCTCTGAGGT 59.921 63.158 4.59 0.00 0.00 3.85
921 1222 2.534396 AACTCCCATCGGCCCAACA 61.534 57.895 0.00 0.00 0.00 3.33
1108 1417 3.997400 CTCCTCTCGTCCCTCGCCA 62.997 68.421 0.00 0.00 39.67 5.69
1227 1537 4.821589 CGCCAACCTCCGGAGCTC 62.822 72.222 26.87 4.71 0.00 4.09
1244 1554 2.202663 CTGCTCTGCTTCGCGCTA 60.203 61.111 5.56 0.00 40.11 4.26
1246 1556 2.507102 GCTCTGCTTCGCGCTACA 60.507 61.111 5.56 0.00 40.11 2.74
1301 1624 3.637297 CGAAGTCGCCCCTTAGTAC 57.363 57.895 0.00 0.00 0.00 2.73
1302 1625 0.101939 CGAAGTCGCCCCTTAGTACC 59.898 60.000 0.00 0.00 0.00 3.34
1311 1649 3.576982 CGCCCCTTAGTACCAATCAGATA 59.423 47.826 0.00 0.00 0.00 1.98
1351 1689 3.445096 AGCCCAGCTGATAAATTTGACAC 59.555 43.478 17.39 0.00 37.57 3.67
1421 1759 0.745845 GCATGGAGTTCACTCGGCAT 60.746 55.000 10.34 3.48 43.76 4.40
1503 1841 0.249955 CACCCCCAACATTGCCATTC 59.750 55.000 0.00 0.00 0.00 2.67
1576 1914 1.168714 GGCAGATCTTCCGCAAGTTT 58.831 50.000 0.00 0.00 0.00 2.66
1583 1921 1.507141 CTTCCGCAAGTTTGACGGCT 61.507 55.000 17.15 0.00 43.00 5.52
1669 2007 0.390860 CGCTCTCCGGATCCATTCTT 59.609 55.000 13.41 0.00 0.00 2.52
1713 2051 4.021981 GCAGGAAGGCATGTTTAGTTCTTT 60.022 41.667 0.00 0.00 0.00 2.52
1714 2052 5.703876 CAGGAAGGCATGTTTAGTTCTTTC 58.296 41.667 0.00 0.00 0.00 2.62
1715 2053 4.767409 AGGAAGGCATGTTTAGTTCTTTCC 59.233 41.667 0.00 0.00 0.00 3.13
1716 2054 4.522789 GGAAGGCATGTTTAGTTCTTTCCA 59.477 41.667 0.00 0.00 0.00 3.53
1720 2059 5.183904 AGGCATGTTTAGTTCTTTCCATGTC 59.816 40.000 0.00 0.00 35.68 3.06
1758 2098 2.519963 CATATCGCTGCATACGTCGAT 58.480 47.619 11.56 11.56 43.12 3.59
1760 2100 0.387367 ATCGCTGCATACGTCGATCC 60.387 55.000 0.00 0.00 37.09 3.36
1786 2126 4.975502 TGACGATTGTTTTGTGCAGATTTC 59.024 37.500 0.00 0.00 0.00 2.17
1787 2127 4.930963 ACGATTGTTTTGTGCAGATTTCA 58.069 34.783 0.00 0.00 0.00 2.69
1913 2253 3.003173 AGCTTGGCGGTAGCTCCA 61.003 61.111 0.00 0.00 45.52 3.86
1951 2291 4.599041 TGGAAAACAAGATACTGATGGGG 58.401 43.478 0.00 0.00 0.00 4.96
1963 2303 0.902984 TGATGGGGCACGAGTGTAGT 60.903 55.000 5.07 0.00 0.00 2.73
2239 2579 1.274167 CCTGATGCAATTGGTGTGCTT 59.726 47.619 7.72 0.00 42.69 3.91
2397 2737 6.252233 TCATGTTCAGGTTCCATTTTATCCA 58.748 36.000 0.00 0.00 0.00 3.41
2423 2763 7.149569 CTCAGCAGATGTTTGAGGATTTTAA 57.850 36.000 7.97 0.00 35.75 1.52
2435 2785 6.855763 TGAGGATTTTAATGCAAAGGTGAT 57.144 33.333 0.00 0.00 0.00 3.06
2436 2786 7.243604 TGAGGATTTTAATGCAAAGGTGATT 57.756 32.000 0.00 0.00 0.00 2.57
2437 2787 7.678837 TGAGGATTTTAATGCAAAGGTGATTT 58.321 30.769 0.00 0.00 0.00 2.17
2438 2788 7.818930 TGAGGATTTTAATGCAAAGGTGATTTC 59.181 33.333 0.00 0.00 0.00 2.17
2439 2789 7.678837 AGGATTTTAATGCAAAGGTGATTTCA 58.321 30.769 0.00 0.00 0.00 2.69
2440 2790 7.820872 AGGATTTTAATGCAAAGGTGATTTCAG 59.179 33.333 0.00 0.00 0.00 3.02
2441 2791 7.603784 GGATTTTAATGCAAAGGTGATTTCAGT 59.396 33.333 0.00 0.00 0.00 3.41
2442 2792 8.907222 ATTTTAATGCAAAGGTGATTTCAGTT 57.093 26.923 0.00 0.00 0.00 3.16
2443 2793 7.712264 TTTAATGCAAAGGTGATTTCAGTTG 57.288 32.000 0.00 0.00 0.00 3.16
2444 2794 5.534207 AATGCAAAGGTGATTTCAGTTGA 57.466 34.783 0.00 0.00 0.00 3.18
2509 2859 5.899120 TCACCTGTGAACATCTACTACTC 57.101 43.478 0.00 0.00 36.53 2.59
2510 2860 4.705507 TCACCTGTGAACATCTACTACTCC 59.294 45.833 0.00 0.00 36.53 3.85
2511 2861 4.024670 ACCTGTGAACATCTACTACTCCC 58.975 47.826 0.00 0.00 0.00 4.30
2513 2863 4.339814 CCTGTGAACATCTACTACTCCCTC 59.660 50.000 0.00 0.00 0.00 4.30
2515 2865 4.950475 TGTGAACATCTACTACTCCCTCTG 59.050 45.833 0.00 0.00 0.00 3.35
2516 2866 4.951094 GTGAACATCTACTACTCCCTCTGT 59.049 45.833 0.00 0.00 0.00 3.41
2517 2867 6.120905 GTGAACATCTACTACTCCCTCTGTA 58.879 44.000 0.00 0.00 0.00 2.74
2518 2868 6.602406 GTGAACATCTACTACTCCCTCTGTAA 59.398 42.308 0.00 0.00 0.00 2.41
2519 2869 7.122353 GTGAACATCTACTACTCCCTCTGTAAA 59.878 40.741 0.00 0.00 0.00 2.01
2520 2870 7.122353 TGAACATCTACTACTCCCTCTGTAAAC 59.878 40.741 0.00 0.00 0.00 2.01
2521 2871 6.733509 ACATCTACTACTCCCTCTGTAAACT 58.266 40.000 0.00 0.00 0.00 2.66
2522 2872 7.870027 ACATCTACTACTCCCTCTGTAAACTA 58.130 38.462 0.00 0.00 0.00 2.24
2523 2873 8.334734 ACATCTACTACTCCCTCTGTAAACTAA 58.665 37.037 0.00 0.00 0.00 2.24
2524 2874 9.357161 CATCTACTACTCCCTCTGTAAACTAAT 57.643 37.037 0.00 0.00 0.00 1.73
2532 2882 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2533 2883 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2534 2884 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2535 2885 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2536 2886 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2585 2935 9.490379 AACGCTCTTATATTAATTTACAGAGGG 57.510 33.333 21.96 21.96 42.53 4.30
2586 2936 8.867097 ACGCTCTTATATTAATTTACAGAGGGA 58.133 33.333 25.54 1.67 40.49 4.20
2587 2937 9.360093 CGCTCTTATATTAATTTACAGAGGGAG 57.640 37.037 20.74 5.24 40.49 4.30
2625 2976 1.486726 ACCCAGTCTGTATAGCCTTGC 59.513 52.381 0.00 0.00 0.00 4.01
2700 3051 8.496751 GTCCTTACAGTTCTGAAATACTTGTTC 58.503 37.037 6.83 0.00 0.00 3.18
2757 3108 4.514066 CCAATATTTACACGCCTCCTTACC 59.486 45.833 0.00 0.00 0.00 2.85
2762 3113 0.323957 ACACGCCTCCTTACCCTTTC 59.676 55.000 0.00 0.00 0.00 2.62
2894 3245 2.030540 GCATGCTGAAGTTGCAGAGAAA 60.031 45.455 11.37 0.00 44.04 2.52
3071 3422 4.910195 AGAAATGTGCACTTCCTGACATA 58.090 39.130 19.41 0.00 0.00 2.29
3259 3611 9.319143 ACATCTCTGCTACAAATATACTGAAAC 57.681 33.333 0.00 0.00 0.00 2.78
3260 3612 9.539825 CATCTCTGCTACAAATATACTGAAACT 57.460 33.333 0.00 0.00 0.00 2.66
3354 3707 2.772515 GTCTATTCCTGCTACCCTTGGT 59.227 50.000 0.00 0.00 40.16 3.67
3399 3752 1.907255 GGTAAAGTACCCTGCTCCTGT 59.093 52.381 0.00 0.00 43.18 4.00
3580 3933 7.523380 GCCTAGGATCAATCATTCCAAGAAATG 60.523 40.741 14.75 0.00 37.87 2.32
3848 4202 5.477291 GGAATACATGAGTAGATCCCTTCGA 59.523 44.000 0.00 0.00 35.59 3.71
3911 4265 7.565398 AGGCAAGTTTCTGACCTAGATCTAATA 59.435 37.037 3.57 0.00 34.80 0.98
4021 4375 4.877773 AGAGGTCATCAGGAGAGTACATT 58.122 43.478 0.00 0.00 0.00 2.71
4181 4535 1.825474 CGTGATGACTCCTTACAGGGT 59.175 52.381 0.00 0.00 35.59 4.34
4282 4636 0.178998 CTTGCCCAGGCTATGCTGAT 60.179 55.000 10.58 0.00 42.51 2.90
4459 4813 2.304761 GGTGGGAGATGTGTCAGGTAAA 59.695 50.000 0.00 0.00 0.00 2.01
4465 4819 6.177610 GGGAGATGTGTCAGGTAAATAACAA 58.822 40.000 0.00 0.00 0.00 2.83
4565 4919 5.535406 AGACGTTAGGAGAGTCTTTTCTCAA 59.465 40.000 0.00 0.00 44.34 3.02
4619 4973 6.236409 AGAATGCCCAGATATACATTCAGTG 58.764 40.000 14.81 0.00 46.90 3.66
4646 5000 4.021102 CTGGGTTCCAGTGTCAATAAGT 57.979 45.455 5.82 0.00 45.82 2.24
4647 5001 5.160607 CTGGGTTCCAGTGTCAATAAGTA 57.839 43.478 5.82 0.00 45.82 2.24
4648 5002 5.745227 CTGGGTTCCAGTGTCAATAAGTAT 58.255 41.667 5.82 0.00 45.82 2.12
4676 5030 2.044555 CCTCGGCCACTAGACGTGA 61.045 63.158 2.24 0.00 46.81 4.35
4677 5031 1.136984 CTCGGCCACTAGACGTGAC 59.863 63.158 2.24 0.00 46.81 3.67
4678 5032 1.583495 CTCGGCCACTAGACGTGACA 61.583 60.000 2.24 0.00 46.81 3.58
4774 5143 6.244654 TCATACATTTGACATGAACTTCCCA 58.755 36.000 0.00 0.00 0.00 4.37
4868 5238 4.202245 TGTACTAATCAACAGGGAGTGC 57.798 45.455 0.00 0.00 0.00 4.40
4900 5270 7.859875 CCAAGTGTTTTTGTTGTGATTTGTTTT 59.140 29.630 0.00 0.00 0.00 2.43
4901 5271 8.680261 CAAGTGTTTTTGTTGTGATTTGTTTTG 58.320 29.630 0.00 0.00 0.00 2.44
4923 5299 4.141367 TGTTACACTGAACCCCAAGAATCA 60.141 41.667 0.00 0.00 0.00 2.57
4984 5361 7.581213 TTTATTATGCACTAAACCCCATGAG 57.419 36.000 0.00 0.00 0.00 2.90
4992 5369 5.803470 GCACTAAACCCCATGAGTTCTAACT 60.803 44.000 0.00 0.00 43.16 2.24
4993 5370 6.238648 CACTAAACCCCATGAGTTCTAACTT 58.761 40.000 0.00 0.00 39.88 2.66
5027 5404 6.255887 CCTATCTAAACAGGCGTAAAGAACAG 59.744 42.308 0.00 0.00 0.00 3.16
5077 5454 3.406764 CAGCCACTTTCTAGCTTTCACT 58.593 45.455 0.00 0.00 33.70 3.41
5148 5525 9.113838 GAGAACATCACCTGAACATACAATTAT 57.886 33.333 0.00 0.00 0.00 1.28
5242 5619 2.547211 CACAGAAACACCAGAGAAGCTG 59.453 50.000 0.00 0.00 44.49 4.24
5264 5641 3.587923 CTTCTTCTCAGGTCTCTGCAAG 58.412 50.000 0.00 0.00 40.69 4.01
5314 5692 2.745821 ACAGCAGCATCATACAACACTG 59.254 45.455 0.00 0.00 0.00 3.66
5413 5791 6.827586 ATTTGAGTGGGCGATAAGTTTTTA 57.172 33.333 0.00 0.00 0.00 1.52
5444 5831 1.678970 GAAGGGCAGAACGGGCAAT 60.679 57.895 0.00 0.00 34.52 3.56
5461 5848 1.945394 CAATTAAGCTCAGCTGGCGAT 59.055 47.619 15.13 12.56 39.62 4.58
5513 5900 5.447279 CGCTTTCGAATTGCCAAACTATACT 60.447 40.000 15.05 0.00 38.10 2.12
5522 5911 9.516314 GAATTGCCAAACTATACTAAAATGGAC 57.484 33.333 0.00 0.00 0.00 4.02
5544 5933 4.586001 ACAATGAAAAGGACACTTGAGCAT 59.414 37.500 0.00 0.00 36.93 3.79
5556 5945 0.907704 TTGAGCATACCTGGGTCGGT 60.908 55.000 0.00 0.00 41.10 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 60 1.136891 GTTGCCAAACAGAAACCAGCT 59.863 47.619 0.00 0.00 36.24 4.24
147 151 0.471617 AGCAACCACAGAAGAGCACT 59.528 50.000 0.00 0.00 0.00 4.40
200 204 1.079127 CATCGTCACCACCTGGACC 60.079 63.158 0.00 0.00 38.94 4.46
242 246 0.533531 TTGTGCTGACTGTGCAGAGG 60.534 55.000 16.19 0.00 41.41 3.69
243 247 0.866427 CTTGTGCTGACTGTGCAGAG 59.134 55.000 9.74 9.74 41.41 3.35
245 249 0.585357 GACTTGTGCTGACTGTGCAG 59.415 55.000 0.00 0.00 41.41 4.41
251 255 0.399454 ATGCAGGACTTGTGCTGACT 59.601 50.000 23.01 8.42 41.78 3.41
255 259 4.338879 AGAAAATATGCAGGACTTGTGCT 58.661 39.130 0.00 0.00 41.78 4.40
258 262 6.040842 ACACAAAGAAAATATGCAGGACTTGT 59.959 34.615 0.00 0.00 0.00 3.16
277 281 1.360820 TTGACGACGAGCAACACAAA 58.639 45.000 0.00 0.00 0.00 2.83
406 410 5.642063 CCAGACTAAACCGATACAACACAAT 59.358 40.000 0.00 0.00 0.00 2.71
426 431 5.414454 CCTGATTAATTGACGGAAAACCAGA 59.586 40.000 0.00 0.00 0.00 3.86
446 451 8.609617 TGATTAAGAGGAAGAGAATTACCTGA 57.390 34.615 0.00 0.00 32.53 3.86
451 456 9.938280 TTTCGTTGATTAAGAGGAAGAGAATTA 57.062 29.630 0.00 0.00 0.00 1.40
462 467 5.163854 ACTCGCCATTTTCGTTGATTAAGAG 60.164 40.000 0.00 0.00 0.00 2.85
483 488 3.963383 TTGAAACGAGGCAAAAGACTC 57.037 42.857 0.00 0.00 0.00 3.36
523 528 7.849804 AAGTTCATGTAGGTTTGCTATGTAG 57.150 36.000 0.00 0.00 0.00 2.74
524 529 8.630054 AAAAGTTCATGTAGGTTTGCTATGTA 57.370 30.769 0.00 0.00 0.00 2.29
525 530 7.524717 AAAAGTTCATGTAGGTTTGCTATGT 57.475 32.000 0.00 0.00 0.00 2.29
602 701 2.279073 CAGTCCGGGGCCTAGAGA 59.721 66.667 0.84 0.00 0.00 3.10
738 837 1.760086 CTCTGCCTCGACCCCTCAT 60.760 63.158 0.00 0.00 0.00 2.90
784 883 4.476752 GACATGGCCGGCGGGTAA 62.477 66.667 29.48 3.34 34.97 2.85
845 944 1.359474 AGAAGGCAGGTACCTCAGAGA 59.641 52.381 12.84 0.00 39.93 3.10
921 1222 1.494824 AGAACGCGTACGAAAAAGCT 58.505 45.000 21.65 4.74 43.93 3.74
1296 1619 8.727100 ATCCACTGAATATCTGATTGGTACTA 57.273 34.615 0.00 0.00 0.00 1.82
1299 1622 7.616528 TGATCCACTGAATATCTGATTGGTA 57.383 36.000 0.00 0.00 0.00 3.25
1300 1623 6.505048 TGATCCACTGAATATCTGATTGGT 57.495 37.500 0.00 0.00 0.00 3.67
1301 1624 7.148457 CGATTGATCCACTGAATATCTGATTGG 60.148 40.741 0.00 0.00 0.00 3.16
1302 1625 7.148457 CCGATTGATCCACTGAATATCTGATTG 60.148 40.741 0.00 0.00 0.00 2.67
1311 1649 2.486191 GGCTCCGATTGATCCACTGAAT 60.486 50.000 0.00 0.00 0.00 2.57
1351 1689 2.781646 GCGAGGTTTCAACAAAACGAAG 59.218 45.455 0.00 0.00 46.85 3.79
1394 1732 2.094286 AGTGAACTCCATGCTTCTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
1421 1759 1.523711 GATGAAATGCGCTCGGGGA 60.524 57.895 9.73 0.00 0.00 4.81
1503 1841 0.029300 CAACACACACGAAAGGCTGG 59.971 55.000 0.00 0.00 0.00 4.85
1583 1921 1.612146 TCTCGATGTCCCAGGCCAA 60.612 57.895 5.01 0.00 0.00 4.52
1589 1927 1.758514 GAGCCCTCTCGATGTCCCA 60.759 63.158 0.00 0.00 0.00 4.37
1669 2007 2.849294 TCATGTGATCAACCGAACCA 57.151 45.000 0.00 0.00 0.00 3.67
1713 2051 1.618343 ACATCACACACTCGACATGGA 59.382 47.619 0.00 0.00 0.00 3.41
1714 2052 2.084610 ACATCACACACTCGACATGG 57.915 50.000 0.00 0.00 0.00 3.66
1715 2053 4.213674 CAAAACATCACACACTCGACATG 58.786 43.478 0.00 0.00 0.00 3.21
1716 2054 3.303990 GCAAAACATCACACACTCGACAT 60.304 43.478 0.00 0.00 0.00 3.06
1720 2059 2.753989 TGCAAAACATCACACACTCG 57.246 45.000 0.00 0.00 0.00 4.18
1758 2098 1.262950 CACAAAACAATCGTCAGCGGA 59.737 47.619 0.00 0.00 38.89 5.54
1760 2100 1.044725 GCACAAAACAATCGTCAGCG 58.955 50.000 0.00 0.00 39.92 5.18
1786 2126 6.868864 CCGATATAGGACTAATGACCTTGTTG 59.131 42.308 0.00 0.00 39.06 3.33
1787 2127 6.553852 ACCGATATAGGACTAATGACCTTGTT 59.446 38.462 9.09 0.00 39.06 2.83
1913 2253 2.574006 TCCAGCAGCAAATCTTGAGT 57.426 45.000 0.00 0.00 0.00 3.41
1951 2291 2.668457 CTGAATGGAACTACACTCGTGC 59.332 50.000 0.00 0.00 0.00 5.34
1963 2303 1.554617 TCATCGGTCAGCTGAATGGAA 59.445 47.619 20.19 2.90 33.10 3.53
2024 2364 0.322975 TGAAGCTTCCTCTCCTGCAC 59.677 55.000 23.42 0.00 0.00 4.57
2077 2417 0.040958 CCAACTCACGCACTTTGCTC 60.041 55.000 0.00 0.00 42.25 4.26
2239 2579 1.376086 CTCCAGGTCATGTGCCACA 59.624 57.895 0.00 0.00 0.00 4.17
2423 2763 5.534207 TTCAACTGAAATCACCTTTGCAT 57.466 34.783 0.00 0.00 0.00 3.96
2507 2857 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2508 2858 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2509 2859 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2510 2860 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2559 2909 9.490379 CCCTCTGTAAATTAATATAAGAGCGTT 57.510 33.333 9.98 0.00 0.00 4.84
2560 2910 8.867097 TCCCTCTGTAAATTAATATAAGAGCGT 58.133 33.333 9.98 0.00 0.00 5.07
2561 2911 9.360093 CTCCCTCTGTAAATTAATATAAGAGCG 57.640 37.037 9.98 4.77 0.00 5.03
2576 2926 9.158233 CGAACATAATTTTTACTCCCTCTGTAA 57.842 33.333 0.00 0.00 0.00 2.41
2577 2927 7.767198 CCGAACATAATTTTTACTCCCTCTGTA 59.233 37.037 0.00 0.00 0.00 2.74
2578 2928 6.598064 CCGAACATAATTTTTACTCCCTCTGT 59.402 38.462 0.00 0.00 0.00 3.41
2579 2929 6.458342 GCCGAACATAATTTTTACTCCCTCTG 60.458 42.308 0.00 0.00 0.00 3.35
2580 2930 5.589050 GCCGAACATAATTTTTACTCCCTCT 59.411 40.000 0.00 0.00 0.00 3.69
2581 2931 5.355910 TGCCGAACATAATTTTTACTCCCTC 59.644 40.000 0.00 0.00 0.00 4.30
2582 2932 5.124936 GTGCCGAACATAATTTTTACTCCCT 59.875 40.000 0.00 0.00 0.00 4.20
2583 2933 5.337554 GTGCCGAACATAATTTTTACTCCC 58.662 41.667 0.00 0.00 0.00 4.30
2584 2934 5.337554 GGTGCCGAACATAATTTTTACTCC 58.662 41.667 0.00 0.00 0.00 3.85
2585 2935 5.106078 TGGGTGCCGAACATAATTTTTACTC 60.106 40.000 0.00 0.00 0.00 2.59
2586 2936 4.767928 TGGGTGCCGAACATAATTTTTACT 59.232 37.500 0.00 0.00 0.00 2.24
2587 2937 5.061920 TGGGTGCCGAACATAATTTTTAC 57.938 39.130 0.00 0.00 0.00 2.01
2588 2938 4.767928 ACTGGGTGCCGAACATAATTTTTA 59.232 37.500 0.00 0.00 0.00 1.52
2589 2939 3.576550 ACTGGGTGCCGAACATAATTTTT 59.423 39.130 0.00 0.00 0.00 1.94
2590 2940 3.161866 ACTGGGTGCCGAACATAATTTT 58.838 40.909 0.00 0.00 0.00 1.82
2591 2941 2.752903 GACTGGGTGCCGAACATAATTT 59.247 45.455 0.00 0.00 0.00 1.82
2592 2942 2.026262 AGACTGGGTGCCGAACATAATT 60.026 45.455 0.00 0.00 0.00 1.40
2593 2943 1.559682 AGACTGGGTGCCGAACATAAT 59.440 47.619 0.00 0.00 0.00 1.28
2594 2944 0.981183 AGACTGGGTGCCGAACATAA 59.019 50.000 0.00 0.00 0.00 1.90
2595 2945 0.249120 CAGACTGGGTGCCGAACATA 59.751 55.000 0.00 0.00 0.00 2.29
2596 2946 1.003355 CAGACTGGGTGCCGAACAT 60.003 57.895 0.00 0.00 0.00 2.71
2597 2947 1.116536 TACAGACTGGGTGCCGAACA 61.117 55.000 7.51 0.00 0.00 3.18
2598 2948 0.249398 ATACAGACTGGGTGCCGAAC 59.751 55.000 7.51 0.00 0.00 3.95
2599 2949 1.754803 CTATACAGACTGGGTGCCGAA 59.245 52.381 7.51 0.00 0.00 4.30
2625 2976 5.192327 ACAGAACAAGCATTTCAGAAAGG 57.808 39.130 3.04 3.04 0.00 3.11
2700 3051 6.449635 ACTCTGCAGACTAGAAATCTACAG 57.550 41.667 13.74 0.00 38.46 2.74
2768 3119 8.511126 ACCTAGAACCAAATGGGAAATACATAT 58.489 33.333 4.17 0.00 41.15 1.78
2781 3132 2.699954 CTCGCACACCTAGAACCAAAT 58.300 47.619 0.00 0.00 0.00 2.32
2894 3245 1.599071 CGATTGTCGCAGCCAACATAT 59.401 47.619 0.00 0.00 31.14 1.78
3071 3422 3.057315 CCAGTGTTCATTCCTGCGAAAAT 60.057 43.478 0.00 0.00 0.00 1.82
3354 3707 3.896888 AGTTTGCAATGGTTGGATCAAGA 59.103 39.130 0.00 0.00 0.00 3.02
3399 3752 2.584835 AATTGTGCACAGCCCTCTTA 57.415 45.000 20.59 2.44 0.00 2.10
3477 3830 5.348164 GGCAAGTTACAAACATTCAACTGT 58.652 37.500 0.00 0.00 31.80 3.55
3848 4202 6.286240 TGGTGAGAATATAGCATTATCGCT 57.714 37.500 5.48 0.00 46.26 4.93
3911 4265 3.354948 TCCATAGCTGAAAGTGCACAT 57.645 42.857 21.04 3.48 35.30 3.21
4021 4375 2.708861 TGAACCAACCTTAGCAGAAGGA 59.291 45.455 20.92 0.00 39.81 3.36
4238 4592 2.936919 ATGACTCTTTCAGTGGTGCA 57.063 45.000 0.00 0.00 37.77 4.57
4282 4636 4.597404 AGCTCGAATTCATCTGCTATCA 57.403 40.909 6.22 0.00 34.97 2.15
4465 4819 5.836358 TCAGGCCTAACCAAAATAACACTTT 59.164 36.000 3.98 0.00 43.14 2.66
4509 4863 1.002430 TCTCACCATGTCAGGTTCTGC 59.998 52.381 0.00 0.00 40.77 4.26
4565 4919 6.070251 CCTGGGGCCTATTTAAACTCAAAATT 60.070 38.462 0.84 0.00 0.00 1.82
4641 4995 6.552350 TGGCCGAGGTTCTAAGTTATACTTAT 59.448 38.462 0.00 0.00 39.68 1.73
4642 4996 5.893255 TGGCCGAGGTTCTAAGTTATACTTA 59.107 40.000 0.00 0.00 39.51 2.24
4643 4997 4.713321 TGGCCGAGGTTCTAAGTTATACTT 59.287 41.667 0.00 0.00 41.97 2.24
4644 4998 4.099113 GTGGCCGAGGTTCTAAGTTATACT 59.901 45.833 0.00 0.00 0.00 2.12
4645 4999 4.099113 AGTGGCCGAGGTTCTAAGTTATAC 59.901 45.833 0.00 0.00 0.00 1.47
4646 5000 4.284178 AGTGGCCGAGGTTCTAAGTTATA 58.716 43.478 0.00 0.00 0.00 0.98
4647 5001 3.105283 AGTGGCCGAGGTTCTAAGTTAT 58.895 45.455 0.00 0.00 0.00 1.89
4648 5002 2.532843 AGTGGCCGAGGTTCTAAGTTA 58.467 47.619 0.00 0.00 0.00 2.24
4868 5238 4.388469 CACAACAAAAACACTTGGTCCAAG 59.612 41.667 27.09 27.09 45.85 3.61
4900 5270 3.935818 TTCTTGGGGTTCAGTGTAACA 57.064 42.857 7.46 0.00 41.43 2.41
4901 5271 4.394729 TGATTCTTGGGGTTCAGTGTAAC 58.605 43.478 0.00 0.00 0.00 2.50
4984 5361 3.636153 AGGGATGGCTCAAGTTAGAAC 57.364 47.619 0.00 0.00 0.00 3.01
4992 5369 4.103153 CCTGTTTAGATAGGGATGGCTCAA 59.897 45.833 0.00 0.00 30.92 3.02
4993 5370 3.648067 CCTGTTTAGATAGGGATGGCTCA 59.352 47.826 0.00 0.00 30.92 4.26
5027 5404 9.894783 TCACTAGTTATAATGTCTCGCTAATTC 57.105 33.333 0.00 0.00 0.00 2.17
5117 5494 1.649321 TCAGGTGATGTTCTCAGGCT 58.351 50.000 0.00 0.00 33.51 4.58
5242 5619 1.274728 TGCAGAGACCTGAGAAGAAGC 59.725 52.381 0.00 0.00 43.02 3.86
5264 5641 1.399791 GTGCAGGAGAATTGCTAGTGC 59.600 52.381 0.00 0.00 42.02 4.40
5383 5761 1.010419 CGCCCACTCAAATTTGCTGC 61.010 55.000 13.54 9.54 0.00 5.25
5384 5762 0.597568 TCGCCCACTCAAATTTGCTG 59.402 50.000 13.54 10.36 0.00 4.41
5413 5791 0.759346 GCCCTTCCATGATCGTACCT 59.241 55.000 0.00 0.00 0.00 3.08
5444 5831 0.528466 CGATCGCCAGCTGAGCTTAA 60.528 55.000 17.39 5.85 36.40 1.85
5461 5848 0.954449 TTTTTACCGCGATTGCCCGA 60.954 50.000 8.23 0.00 38.08 5.14
5467 5854 4.612712 CGATGCCATATTTTTACCGCGATT 60.613 41.667 8.23 0.00 0.00 3.34
5499 5886 8.410673 TTGTCCATTTTAGTATAGTTTGGCAA 57.589 30.769 0.00 0.00 0.00 4.52
5513 5900 7.595819 AGTGTCCTTTTCATTGTCCATTTTA 57.404 32.000 0.00 0.00 0.00 1.52
5522 5911 4.572985 TGCTCAAGTGTCCTTTTCATTG 57.427 40.909 0.00 0.00 0.00 2.82
5544 5933 1.332144 GCCATACACCGACCCAGGTA 61.332 60.000 0.00 0.00 43.89 3.08
5556 5945 2.745281 GCGTGAACTTTTAGGCCATACA 59.255 45.455 5.01 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.