Multiple sequence alignment - TraesCS6D01G222700

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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 TraesCS6D01G222700 chr6D 100.000 7450 0 0 1 7450 314092878 314085429 0.000000e+00 13758.0
1 TraesCS6D01G222700 chr6D 89.362 141 15 0 1713 1853 731562 731702 2.140000e-40 178.0
2 TraesCS6D01G222700 chr6A 93.857 2930 93 32 3269 6138 451666920 451664018 0.000000e+00 4333.0
3 TraesCS6D01G222700 chr6A 96.054 2230 52 15 777 2988 451669128 451666917 0.000000e+00 3598.0
4 TraesCS6D01G222700 chr6A 92.182 1343 70 14 6135 7450 451663975 451662641 0.000000e+00 1866.0
5 TraesCS6D01G222700 chr6B 94.922 2619 61 23 2616 5164 512435790 512438406 0.000000e+00 4034.0
6 TraesCS6D01G222700 chr6B 94.341 1714 80 8 1 1713 512433042 512434739 0.000000e+00 2612.0
7 TraesCS6D01G222700 chr6B 93.579 1464 66 16 5996 7450 512439246 512440690 0.000000e+00 2158.0
8 TraesCS6D01G222700 chr6B 91.757 461 24 5 2134 2593 512435355 512435802 4.910000e-176 628.0
9 TraesCS6D01G222700 chr6B 95.308 341 12 3 5574 5910 512438918 512439258 8.510000e-149 538.0
10 TraesCS6D01G222700 chr6B 94.737 342 15 3 5166 5506 512438561 512438900 5.120000e-146 529.0
11 TraesCS6D01G222700 chr6B 92.466 292 15 1 1853 2137 512434732 512435023 1.930000e-110 411.0
12 TraesCS6D01G222700 chrUn 100.000 406 0 0 4432 4837 478091423 478091828 0.000000e+00 750.0
13 TraesCS6D01G222700 chrUn 89.928 139 13 1 1714 1852 322032047 322032184 2.140000e-40 178.0
14 TraesCS6D01G222700 chrUn 95.181 83 4 0 2885 2967 253162580 253162498 1.690000e-26 132.0
15 TraesCS6D01G222700 chr1D 92.647 136 5 4 1725 1856 289565140 289565274 2.740000e-44 191.0
16 TraesCS6D01G222700 chr4D 91.304 138 7 4 1725 1858 30845383 30845247 4.590000e-42 183.0
17 TraesCS6D01G222700 chr4B 89.928 139 13 1 1714 1852 660413652 660413789 2.140000e-40 178.0
18 TraesCS6D01G222700 chr4B 89.928 139 13 1 1714 1852 660426655 660426792 2.140000e-40 178.0
19 TraesCS6D01G222700 chr4B 89.928 139 13 1 1714 1852 660438467 660438604 2.140000e-40 178.0
20 TraesCS6D01G222700 chr4B 95.181 83 4 0 2885 2967 517165113 517165031 1.690000e-26 132.0
21 TraesCS6D01G222700 chr1B 89.362 141 14 1 1714 1853 542758728 542758588 7.680000e-40 176.0
22 TraesCS6D01G222700 chr1B 81.013 158 24 4 1707 1859 10048903 10049059 3.650000e-23 121.0
23 TraesCS6D01G222700 chr7B 83.750 160 12 5 1725 1870 129311169 129311010 1.010000e-28 139.0
24 TraesCS6D01G222700 chr7B 74.479 192 44 5 25 213 443138045 443137856 2.230000e-10 78.7
25 TraesCS6D01G222700 chr2B 95.294 85 4 0 2883 2967 391762413 391762329 1.300000e-27 135.0
26 TraesCS6D01G222700 chr1A 95.294 85 4 0 2883 2967 335024192 335024276 1.300000e-27 135.0
27 TraesCS6D01G222700 chr1A 86.765 68 7 2 3138 3204 99009372 99009438 2.880000e-09 75.0
28 TraesCS6D01G222700 chr1A 94.595 37 2 0 3064 3100 85313907 85313943 2.900000e-04 58.4
29 TraesCS6D01G222700 chr3D 95.238 84 4 0 2884 2967 147832158 147832241 4.690000e-27 134.0
30 TraesCS6D01G222700 chr3B 95.238 84 4 0 2884 2967 214549830 214549747 4.690000e-27 134.0
31 TraesCS6D01G222700 chr3B 97.368 38 1 0 3063 3100 790465756 790465719 1.740000e-06 65.8
32 TraesCS6D01G222700 chr7A 76.763 241 47 7 3 241 641240589 641240822 7.850000e-25 126.0
33 TraesCS6D01G222700 chr5A 90.426 94 8 1 2874 2967 37838537 37838445 1.020000e-23 122.0
34 TraesCS6D01G222700 chr5A 85.057 87 11 2 120 205 330228402 330228317 3.700000e-13 87.9
35 TraesCS6D01G222700 chr5A 97.297 37 1 0 3064 3100 225246147 225246183 6.240000e-06 63.9
36 TraesCS6D01G222700 chr2D 89.855 69 7 0 137 205 2787663 2787595 1.030000e-13 89.8
37 TraesCS6D01G222700 chr2D 97.059 34 1 0 751 784 143255676 143255709 2.900000e-04 58.4
38 TraesCS6D01G222700 chr7D 83.871 93 11 4 1776 1866 446986870 446986780 1.330000e-12 86.1
39 TraesCS6D01G222700 chr5B 82.222 90 14 2 543 631 467226272 467226360 8.020000e-10 76.8


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 TraesCS6D01G222700 chr6D 314085429 314092878 7449 True 13758.000000 13758 100.000000 1 7450 1 chr6D.!!$R1 7449
1 TraesCS6D01G222700 chr6A 451662641 451669128 6487 True 3265.666667 4333 94.031000 777 7450 3 chr6A.!!$R1 6673
2 TraesCS6D01G222700 chr6B 512433042 512440690 7648 False 1558.571429 4034 93.872857 1 7450 7 chr6B.!!$F1 7449

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
347 348 0.116342 TCTCCAGTGCCCTTAGGTCA 59.884 55.000 0.00 0.00 34.57 4.02 F
478 479 0.307760 GTGCGTGTGGTTTCCTGAAG 59.692 55.000 0.00 0.00 0.00 3.02 F
772 773 1.004560 TCTTCGGCTTGCTCCAGTG 60.005 57.895 0.00 0.00 0.00 3.66 F
998 999 1.593750 GCAGGCGCGAATCTGATCT 60.594 57.895 22.39 0.00 33.11 2.75 F
999 1000 1.829349 GCAGGCGCGAATCTGATCTG 61.829 60.000 22.39 7.72 33.11 2.90 F
2921 3275 1.394618 AGCCAACGCAACCAAAAGTA 58.605 45.000 0.00 0.00 37.52 2.24 F
3380 3753 0.391597 ACAACACACCGGTCCTACTG 59.608 55.000 2.59 0.87 0.00 2.74 F
3406 3779 0.680921 TTGCTGGTAGCTGCCATTCC 60.681 55.000 24.75 15.35 42.97 3.01 F
3881 4275 3.516615 GTCTTGGTACTCAGTGATCAGC 58.483 50.000 0.00 0.00 0.00 4.26 F
5432 6016 0.734889 GGAGTGGTGCCGATTCATTG 59.265 55.000 0.00 0.00 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1399 1.065126 ACCAGAAGGATTAGCACAGGC 60.065 52.381 0.00 0.0 38.69 4.85 R
1811 1822 2.513897 GCCAAATAGCGGCGGACT 60.514 61.111 9.78 0.0 40.35 3.85 R
1854 1865 3.054213 TGGCATCACATCCTCTCATTTCA 60.054 43.478 0.00 0.0 0.00 2.69 R
2921 3275 0.693049 AGCCCTTTCCATCAGTTCGT 59.307 50.000 0.00 0.0 0.00 3.85 R
2994 3348 0.861155 ATCACGGAGGTCCTATCCCT 59.139 55.000 0.00 0.0 32.86 4.20 R
3881 4275 4.363999 GTCTCCTCCACAAGATTCATACG 58.636 47.826 0.00 0.0 0.00 3.06 R
5325 5905 5.163581 CCATGAATGTGAATTGAGTCTTCCC 60.164 44.000 0.00 0.0 0.00 3.97 R
5401 5985 1.072331 CACCACTCCTGCCAGTTACTT 59.928 52.381 0.00 0.0 0.00 2.24 R
5671 6258 0.104487 TACGGTGCTCGGTTGTTTCA 59.896 50.000 4.24 0.0 44.45 2.69 R
6896 7546 0.106708 TTGACTGAAGCGACTGCCTT 59.893 50.000 0.00 0.0 44.31 4.35 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
18 19 2.704719 ATTGTCTTCCCCGCCCTAA 58.295 52.632 0.00 0.00 0.00 2.69
44 45 6.403636 CCTCATTTAGTTGGTGTGCTTATCAC 60.404 42.308 0.00 0.00 45.82 3.06
85 86 2.589720 TGTGTCTCTGACGGGTCTTTA 58.410 47.619 0.00 0.00 34.95 1.85
91 92 3.695060 TCTCTGACGGGTCTTTAGTCATC 59.305 47.826 0.00 0.00 42.97 2.92
103 104 5.800941 GTCTTTAGTCATCTGGTCAGTTACG 59.199 44.000 0.00 0.00 0.00 3.18
120 121 4.576463 AGTTACGCTTTCAATGGATCCATC 59.424 41.667 27.45 12.73 35.31 3.51
148 149 1.993370 GGTCGTCTTTCATGGTCTTCG 59.007 52.381 0.00 0.00 0.00 3.79
191 192 1.571919 CGTTATCTTCTTCGGGGCAG 58.428 55.000 0.00 0.00 0.00 4.85
236 237 2.179517 GACGTCTCCTGGTCTGCG 59.820 66.667 8.70 0.00 0.00 5.18
246 247 1.013596 CTGGTCTGCGTCAAACAACA 58.986 50.000 0.00 0.00 0.00 3.33
254 255 6.200097 GGTCTGCGTCAAACAACATAATTTTT 59.800 34.615 0.00 0.00 0.00 1.94
279 280 1.892819 ATGTGCTCCCGTGACTCAGG 61.893 60.000 0.00 0.00 0.00 3.86
285 286 1.079127 CCCGTGACTCAGGCGATTT 60.079 57.895 0.00 0.00 0.00 2.17
303 304 1.772836 TTAGGGTTCTCGCCTCCTAC 58.227 55.000 0.00 0.00 32.22 3.18
305 306 0.971447 AGGGTTCTCGCCTCCTACAC 60.971 60.000 0.00 0.00 0.00 2.90
347 348 0.116342 TCTCCAGTGCCCTTAGGTCA 59.884 55.000 0.00 0.00 34.57 4.02
364 365 1.812571 GTCAATGAGGCGTTGTGGATT 59.187 47.619 0.00 0.00 32.76 3.01
380 381 1.795286 GGATTTCGATCCTTGCTAGCG 59.205 52.381 10.77 0.00 37.73 4.26
432 433 5.516090 TCTTTGTGTTCGTTTAGGATTTGC 58.484 37.500 0.00 0.00 0.00 3.68
438 439 1.431845 GTTTAGGATTTGCGCCCCG 59.568 57.895 4.18 0.00 0.00 5.73
451 452 3.787001 CCCCGCTCAGGAAGGTCC 61.787 72.222 0.00 0.00 45.00 4.46
478 479 0.307760 GTGCGTGTGGTTTCCTGAAG 59.692 55.000 0.00 0.00 0.00 3.02
497 498 2.117051 AGACGGAATAAGGTTCTCCCC 58.883 52.381 0.00 0.00 0.00 4.81
573 574 6.378564 AGGTGTATATTCGATGGACTCCATAG 59.621 42.308 10.79 10.96 45.26 2.23
606 607 2.921754 CGTTTGTCTTCGGTGGATCTAC 59.078 50.000 0.00 0.00 0.00 2.59
650 651 6.508563 CGTCTGCATTTGTGTATCTACATGTC 60.509 42.308 0.00 0.00 38.63 3.06
699 700 2.923643 TCGCTTGCGGTTATTGTTTTC 58.076 42.857 15.10 0.00 0.00 2.29
705 706 2.355132 TGCGGTTATTGTTTTCGTGTGT 59.645 40.909 0.00 0.00 0.00 3.72
738 739 5.363101 GGTCTTAGCATGATGACTTGATGA 58.637 41.667 0.00 0.00 0.00 2.92
739 740 5.996513 GGTCTTAGCATGATGACTTGATGAT 59.003 40.000 0.00 0.00 0.00 2.45
740 741 6.485984 GGTCTTAGCATGATGACTTGATGATT 59.514 38.462 0.00 0.00 0.00 2.57
743 744 3.318275 AGCATGATGACTTGATGATTGCC 59.682 43.478 0.00 0.00 0.00 4.52
763 764 2.506438 GTAGCGCGTCTTCGGCTT 60.506 61.111 8.43 0.00 41.24 4.35
768 769 3.491652 GCGTCTTCGGCTTGCTCC 61.492 66.667 0.00 0.00 37.56 4.70
772 773 1.004560 TCTTCGGCTTGCTCCAGTG 60.005 57.895 0.00 0.00 0.00 3.66
790 791 4.275689 CCAGTGTTTGTAGTCATTGCTTGA 59.724 41.667 0.00 0.00 0.00 3.02
825 826 6.982852 TGTTGTTTTTGGTGTTCTTTCTACA 58.017 32.000 0.00 0.00 0.00 2.74
830 831 2.846193 TGGTGTTCTTTCTACAGCCAC 58.154 47.619 0.00 0.00 41.91 5.01
925 926 2.420687 CCACAATTCCTACTGGCTCCTC 60.421 54.545 0.00 0.00 0.00 3.71
968 969 3.008049 AGCGAGAAGTGTATTCCAAACCT 59.992 43.478 0.00 0.00 0.00 3.50
995 996 2.510012 CTGCAGGCGCGAATCTGA 60.510 61.111 22.39 10.61 42.97 3.27
996 997 1.886313 CTGCAGGCGCGAATCTGAT 60.886 57.895 22.39 0.00 42.97 2.90
997 998 1.829349 CTGCAGGCGCGAATCTGATC 61.829 60.000 22.39 10.37 42.97 2.92
998 999 1.593750 GCAGGCGCGAATCTGATCT 60.594 57.895 22.39 0.00 33.11 2.75
999 1000 1.829349 GCAGGCGCGAATCTGATCTG 61.829 60.000 22.39 7.72 33.11 2.90
1781 1792 7.355778 GCTAAATGGTCTCATGTACAAATAGC 58.644 38.462 0.00 2.57 33.18 2.97
1852 1863 4.385358 AGCCCGCTATTTAAAACATTGG 57.615 40.909 0.00 0.00 0.00 3.16
1853 1864 3.767131 AGCCCGCTATTTAAAACATTGGT 59.233 39.130 0.00 0.00 0.00 3.67
1854 1865 4.221924 AGCCCGCTATTTAAAACATTGGTT 59.778 37.500 0.00 0.00 39.43 3.67
1855 1866 4.328712 GCCCGCTATTTAAAACATTGGTTG 59.671 41.667 0.00 0.00 37.30 3.77
2137 2155 7.817478 TGGGCATATATACTTACAAAGATGACG 59.183 37.037 0.00 0.00 0.00 4.35
2232 2585 7.439056 AGTGTTGTGCAAATTAAATCAGGAAAG 59.561 33.333 0.00 0.00 0.00 2.62
2395 2749 6.112058 AGAAAACTAAATGCTGCCAACAAAA 58.888 32.000 0.00 0.00 0.00 2.44
2424 2778 6.915843 AGGCAGTTTTAATACAGTTTTGAACG 59.084 34.615 0.00 0.00 36.23 3.95
2518 2872 4.077108 CCAGCATACATGGCTATTGACAT 58.923 43.478 0.00 0.00 44.07 3.06
2593 2947 9.602568 TGTGTACTGTTCTACTTGTATTTTCAA 57.397 29.630 0.00 0.00 0.00 2.69
2921 3275 1.394618 AGCCAACGCAACCAAAAGTA 58.605 45.000 0.00 0.00 37.52 2.24
2943 3297 2.168521 CGAACTGATGGAAAGGGCTAGA 59.831 50.000 0.00 0.00 0.00 2.43
2994 3348 0.821711 GCACACCCAGCACCAAGTTA 60.822 55.000 0.00 0.00 0.00 2.24
3072 3426 1.543871 GCTCCCTCCGTTAAAACCACA 60.544 52.381 0.00 0.00 0.00 4.17
3088 3442 9.892130 TTAAAACCACAACAAGTATTTTGGAAT 57.108 25.926 0.00 0.00 32.78 3.01
3091 3445 5.221621 ACCACAACAAGTATTTTGGAATGGG 60.222 40.000 0.00 0.00 0.00 4.00
3143 3497 2.173143 GGACCCCCGTATGTGGAATAAA 59.827 50.000 0.00 0.00 0.00 1.40
3222 3595 7.445707 CCTTTCCCTAGCTCCTAATCAATTAAC 59.554 40.741 0.00 0.00 0.00 2.01
3380 3753 0.391597 ACAACACACCGGTCCTACTG 59.608 55.000 2.59 0.87 0.00 2.74
3406 3779 0.680921 TTGCTGGTAGCTGCCATTCC 60.681 55.000 24.75 15.35 42.97 3.01
3831 4225 4.330944 AAATACTGTCCGTTGAGTGTGA 57.669 40.909 0.00 0.00 0.00 3.58
3881 4275 3.516615 GTCTTGGTACTCAGTGATCAGC 58.483 50.000 0.00 0.00 0.00 4.26
4106 4500 6.309494 CCGTCAAGTAGTCGATCATGTTTTAA 59.691 38.462 0.00 0.00 0.00 1.52
4234 4630 9.944663 GATTTACAGTTTTACACAATGTCAGAA 57.055 29.630 0.00 0.00 0.00 3.02
4392 4788 5.304778 TCAAAGTGCTTAGCATTGTACTGA 58.695 37.500 11.03 5.23 41.91 3.41
5010 5408 6.212791 ACAGGTGAAGCTACCAGTTCTTTATA 59.787 38.462 8.39 0.00 43.37 0.98
5099 5525 9.492973 AGTTTTGAAAATGGTGAAATAGGAATG 57.507 29.630 0.00 0.00 0.00 2.67
5123 5549 6.966066 TGTTACAATGCACGATAATTCATGTG 59.034 34.615 0.00 0.00 35.48 3.21
5133 5559 7.576236 CACGATAATTCATGTGGGATCTTAAC 58.424 38.462 0.00 0.00 0.00 2.01
5254 5833 5.107298 GCAACGATAATTCTAGATGGCTCAC 60.107 44.000 0.00 0.00 0.00 3.51
5325 5905 5.005452 GCAATAAGCAAACAAGGAAAACG 57.995 39.130 0.00 0.00 44.79 3.60
5419 6003 1.611673 CCAAGTAACTGGCAGGAGTGG 60.612 57.143 20.34 13.95 0.00 4.00
5432 6016 0.734889 GGAGTGGTGCCGATTCATTG 59.265 55.000 0.00 0.00 0.00 2.82
5461 6046 3.733443 AAAACTCAATCAACAGGCACC 57.267 42.857 0.00 0.00 0.00 5.01
5518 6104 3.580319 ACCACAAGGGGAGGCCAC 61.580 66.667 5.01 0.00 42.91 5.01
5584 6170 1.683385 GCTGTGCACTCCCTTTTCTTT 59.317 47.619 19.41 0.00 0.00 2.52
5671 6258 5.852282 AGCCGTGGCATTTTTATTTAGAT 57.148 34.783 14.29 0.00 44.88 1.98
5688 6275 0.165944 GATGAAACAACCGAGCACCG 59.834 55.000 0.00 0.00 38.18 4.94
5717 6304 1.305930 GCCAGGCCTCAAACGGTTAG 61.306 60.000 0.00 0.00 0.00 2.34
5766 6353 1.620819 CCACTAGCCAACTGACTGACT 59.379 52.381 0.00 0.00 0.00 3.41
5819 6406 4.768968 GCAGTGATTTATAATGAGGGGCAT 59.231 41.667 0.00 0.00 39.43 4.40
5880 6467 9.972106 AATGATCTCCCAAAAGGATATCTATTC 57.028 33.333 2.05 0.00 46.33 1.75
5885 6472 9.621239 TCTCCCAAAAGGATATCTATTCTGTAT 57.379 33.333 2.05 0.00 46.33 2.29
5926 6516 7.652909 TGATTTCAATAGCTTGTTTTGAAGTGG 59.347 33.333 0.00 0.00 39.67 4.00
5931 6521 3.287222 AGCTTGTTTTGAAGTGGCACTA 58.713 40.909 22.37 2.68 0.00 2.74
5964 6554 9.988350 CATATTAAGTCAGCAAGAAAATAACGT 57.012 29.630 0.00 0.00 0.00 3.99
5966 6556 7.485418 TTAAGTCAGCAAGAAAATAACGTCA 57.515 32.000 0.00 0.00 0.00 4.35
5967 6557 5.344207 AGTCAGCAAGAAAATAACGTCAC 57.656 39.130 0.00 0.00 0.00 3.67
5968 6558 4.814234 AGTCAGCAAGAAAATAACGTCACA 59.186 37.500 0.00 0.00 0.00 3.58
5969 6559 4.904154 GTCAGCAAGAAAATAACGTCACAC 59.096 41.667 0.00 0.00 0.00 3.82
5970 6560 4.572795 TCAGCAAGAAAATAACGTCACACA 59.427 37.500 0.00 0.00 0.00 3.72
5971 6561 5.238432 TCAGCAAGAAAATAACGTCACACAT 59.762 36.000 0.00 0.00 0.00 3.21
5972 6562 5.340403 CAGCAAGAAAATAACGTCACACATG 59.660 40.000 0.00 0.00 0.00 3.21
5973 6563 4.616802 GCAAGAAAATAACGTCACACATGG 59.383 41.667 0.00 0.00 0.00 3.66
5974 6564 5.561919 GCAAGAAAATAACGTCACACATGGA 60.562 40.000 0.00 0.00 0.00 3.41
5975 6565 6.611381 CAAGAAAATAACGTCACACATGGAT 58.389 36.000 0.00 0.00 0.00 3.41
5976 6566 7.625395 GCAAGAAAATAACGTCACACATGGATA 60.625 37.037 0.00 0.00 0.00 2.59
5977 6567 8.397906 CAAGAAAATAACGTCACACATGGATAT 58.602 33.333 0.00 0.00 0.00 1.63
5978 6568 7.919690 AGAAAATAACGTCACACATGGATATG 58.080 34.615 0.00 0.00 40.24 1.78
5980 6570 7.624360 AAATAACGTCACACATGGATATGTT 57.376 32.000 0.00 0.46 45.01 2.71
5981 6571 4.944962 AACGTCACACATGGATATGTTG 57.055 40.909 0.00 0.00 45.01 3.33
5982 6572 3.270027 ACGTCACACATGGATATGTTGG 58.730 45.455 0.00 0.00 45.01 3.77
5983 6573 3.270027 CGTCACACATGGATATGTTGGT 58.730 45.455 0.00 0.00 45.01 3.67
5984 6574 4.081365 ACGTCACACATGGATATGTTGGTA 60.081 41.667 0.00 0.00 45.01 3.25
5985 6575 4.270084 CGTCACACATGGATATGTTGGTAC 59.730 45.833 0.00 0.00 45.01 3.34
5986 6576 5.428253 GTCACACATGGATATGTTGGTACT 58.572 41.667 0.00 0.00 45.01 2.73
5987 6577 5.294306 GTCACACATGGATATGTTGGTACTG 59.706 44.000 0.00 0.00 45.01 2.74
6000 6590 4.202419 TGTTGGTACTGTATGGTTTGCTCT 60.202 41.667 0.00 0.00 0.00 4.09
6293 6932 1.344953 TTGGATGGGTAGCAGGCGAT 61.345 55.000 0.00 0.00 0.00 4.58
6332 6971 3.009143 GTCCTTGGACTGACCCTATTGTT 59.991 47.826 12.20 0.00 38.00 2.83
6703 7344 8.296713 GCACAGGTTCTGAACATCTTAAAAATA 58.703 33.333 21.01 0.00 35.18 1.40
6854 7503 1.563410 TCCATGCATGTACCCATCACA 59.437 47.619 24.58 0.00 0.00 3.58
6889 7539 3.587061 TGTTCTCACACTAATCCCATGGT 59.413 43.478 11.73 0.00 0.00 3.55
6893 7543 6.575244 TCTCACACTAATCCCATGGTAATT 57.425 37.500 11.73 12.33 0.00 1.40
6896 7546 8.553153 TCTCACACTAATCCCATGGTAATTTAA 58.447 33.333 11.73 0.00 0.00 1.52
6911 7561 4.425577 AATTTAAAGGCAGTCGCTTCAG 57.574 40.909 0.00 0.00 38.60 3.02
6912 7562 2.543777 TTAAAGGCAGTCGCTTCAGT 57.456 45.000 0.00 0.00 38.60 3.41
6942 7593 2.123409 GCCCACACAAAGGCTGAAA 58.877 52.632 0.00 0.00 46.14 2.69
7119 7780 8.467963 AATAACATCACAATCAATAGGCATGA 57.532 30.769 0.00 0.00 0.00 3.07
7156 7819 4.141937 TGGTCATAACATCAGTCAGTAGGC 60.142 45.833 0.00 0.00 0.00 3.93
7158 7821 3.068165 TCATAACATCAGTCAGTAGGCGG 59.932 47.826 0.00 0.00 0.00 6.13
7200 7863 3.144657 TGAACAGGAGTTGCATGACAT 57.855 42.857 0.00 0.00 38.30 3.06
7212 7875 4.690184 TGCATGACATTGACAACTGATC 57.310 40.909 0.00 0.00 0.00 2.92
7318 7982 5.422970 AGGGCTTCTTTGATTTGCATGAATA 59.577 36.000 0.00 0.00 0.00 1.75
7326 7990 9.708092 TCTTTGATTTGCATGAATATCAAAACA 57.292 25.926 24.18 15.38 42.86 2.83
7375 8043 4.142038 AGTGGTGTGTTTACTTGAATCCC 58.858 43.478 0.00 0.00 0.00 3.85
7397 8065 5.363580 CCCATAGGATTAGCAAACCAAATGT 59.636 40.000 0.00 0.00 33.47 2.71
7398 8066 6.127083 CCCATAGGATTAGCAAACCAAATGTT 60.127 38.462 0.00 0.00 34.73 2.71
7399 8067 6.980397 CCATAGGATTAGCAAACCAAATGTTC 59.020 38.462 0.00 0.00 35.67 3.18
7400 8068 7.147846 CCATAGGATTAGCAAACCAAATGTTCT 60.148 37.037 0.00 0.00 35.67 3.01
7401 8069 6.029346 AGGATTAGCAAACCAAATGTTCTG 57.971 37.500 0.00 0.00 35.67 3.02
7402 8070 5.774690 AGGATTAGCAAACCAAATGTTCTGA 59.225 36.000 0.00 0.00 35.67 3.27
7404 8072 6.366061 GGATTAGCAAACCAAATGTTCTGAAC 59.634 38.462 13.49 13.49 35.67 3.18
7406 8074 3.450457 AGCAAACCAAATGTTCTGAACCA 59.550 39.130 17.26 6.61 35.67 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.508845 AGCACACCAACTAAATGAGGT 57.491 42.857 0.00 0.00 33.91 3.85
85 86 2.171840 AGCGTAACTGACCAGATGACT 58.828 47.619 3.76 0.00 0.00 3.41
91 92 3.120199 CCATTGAAAGCGTAACTGACCAG 60.120 47.826 0.00 0.00 0.00 4.00
103 104 3.559069 TCCAGATGGATCCATTGAAAGC 58.441 45.455 27.93 14.07 39.78 3.51
120 121 3.127548 CCATGAAAGACGACCAAATCCAG 59.872 47.826 0.00 0.00 0.00 3.86
148 149 4.120589 CGATAAGGGCTTGTAGAAACTCC 58.879 47.826 0.00 0.00 0.00 3.85
254 255 0.612744 TCACGGGAGCACATGATCAA 59.387 50.000 0.00 0.00 30.87 2.57
285 286 0.627451 TGTAGGAGGCGAGAACCCTA 59.373 55.000 0.00 0.00 31.41 3.53
316 317 1.001406 CACTGGAGACAAGACAGACCC 59.999 57.143 0.00 0.00 42.06 4.46
323 324 1.902508 CTAAGGGCACTGGAGACAAGA 59.097 52.381 0.00 0.00 42.06 3.02
347 348 1.468520 CGAAATCCACAACGCCTCATT 59.531 47.619 0.00 0.00 0.00 2.57
364 365 0.815095 TCACGCTAGCAAGGATCGAA 59.185 50.000 16.45 0.00 0.00 3.71
380 381 1.789506 AAACGAAGCAGAGCTCTCAC 58.210 50.000 14.96 9.36 38.25 3.51
402 403 7.267128 TCCTAAACGAACACAAAGAAGACTTA 58.733 34.615 0.00 0.00 35.05 2.24
405 406 5.978934 TCCTAAACGAACACAAAGAAGAC 57.021 39.130 0.00 0.00 0.00 3.01
478 479 1.202498 CGGGGAGAACCTTATTCCGTC 60.202 57.143 0.00 0.00 40.03 4.79
497 498 1.278238 GCCATGACGGAGACTAAACG 58.722 55.000 0.00 0.00 36.56 3.60
573 574 3.471495 AGACAAACGCCAATCGAATTC 57.529 42.857 0.00 0.00 41.67 2.17
699 700 0.661020 GACCCCAAGAACAACACACG 59.339 55.000 0.00 0.00 0.00 4.49
705 706 3.073798 TCATGCTAAGACCCCAAGAACAA 59.926 43.478 0.00 0.00 0.00 2.83
763 764 3.769739 ATGACTACAAACACTGGAGCA 57.230 42.857 0.00 0.00 40.05 4.26
768 769 5.422666 TCAAGCAATGACTACAAACACTG 57.577 39.130 0.00 0.00 31.50 3.66
772 773 7.081526 AGATCATCAAGCAATGACTACAAAC 57.918 36.000 0.00 0.00 41.93 2.93
790 791 7.274447 ACACCAAAAACAACATCAAAGATCAT 58.726 30.769 0.00 0.00 0.00 2.45
825 826 5.952347 TCTGGATCAATATATAGTCGTGGCT 59.048 40.000 0.00 0.00 0.00 4.75
861 862 6.377080 GGGAAAAGGAGGATCAAGGAATTAT 58.623 40.000 0.00 0.00 36.25 1.28
925 926 1.275291 TCTTTGGACAGCTAGGAACCG 59.725 52.381 0.00 0.00 0.00 4.44
995 996 0.541392 TTGTAGTGCGGCCATCAGAT 59.459 50.000 2.24 0.00 0.00 2.90
996 997 0.323302 TTTGTAGTGCGGCCATCAGA 59.677 50.000 2.24 0.00 0.00 3.27
997 998 0.447801 GTTTGTAGTGCGGCCATCAG 59.552 55.000 2.24 0.00 0.00 2.90
998 999 1.295357 CGTTTGTAGTGCGGCCATCA 61.295 55.000 2.24 0.00 0.00 3.07
999 1000 1.423845 CGTTTGTAGTGCGGCCATC 59.576 57.895 2.24 0.00 0.00 3.51
1398 1399 1.065126 ACCAGAAGGATTAGCACAGGC 60.065 52.381 0.00 0.00 38.69 4.85
1521 1523 8.474025 CCAACCTCACTGGCATTTATTTATTTA 58.526 33.333 0.00 0.00 40.22 1.40
1522 1524 7.180051 TCCAACCTCACTGGCATTTATTTATTT 59.820 33.333 0.00 0.00 40.22 1.40
1523 1525 6.667414 TCCAACCTCACTGGCATTTATTTATT 59.333 34.615 0.00 0.00 40.22 1.40
1524 1526 6.194235 TCCAACCTCACTGGCATTTATTTAT 58.806 36.000 0.00 0.00 40.22 1.40
1811 1822 2.513897 GCCAAATAGCGGCGGACT 60.514 61.111 9.78 0.00 40.35 3.85
1852 1863 4.201990 GGCATCACATCCTCTCATTTCAAC 60.202 45.833 0.00 0.00 0.00 3.18
1853 1864 3.949754 GGCATCACATCCTCTCATTTCAA 59.050 43.478 0.00 0.00 0.00 2.69
1854 1865 3.054213 TGGCATCACATCCTCTCATTTCA 60.054 43.478 0.00 0.00 0.00 2.69
1855 1866 3.548770 TGGCATCACATCCTCTCATTTC 58.451 45.455 0.00 0.00 0.00 2.17
2232 2585 7.639039 TCAATTGAACGTTATGCAGGAATATC 58.361 34.615 5.45 0.00 0.00 1.63
2424 2778 6.074676 ACGAGAAAGTGTTCGTTATGTGTTAC 60.075 38.462 0.00 0.00 46.87 2.50
2705 3059 4.765339 CGTACATATGTATCCTGACTCCCA 59.235 45.833 18.27 0.00 32.54 4.37
2822 3176 4.720090 CATATCAGGAATGCGATTCAAGC 58.280 43.478 9.92 0.00 41.03 4.01
2874 3228 7.552459 TGCATGAAGCTTAACAGTACTATACA 58.448 34.615 0.00 0.00 45.94 2.29
2921 3275 0.693049 AGCCCTTTCCATCAGTTCGT 59.307 50.000 0.00 0.00 0.00 3.85
2943 3297 6.061022 TGTTGGAGTGTATATGTGGATTGT 57.939 37.500 0.00 0.00 0.00 2.71
2994 3348 0.861155 ATCACGGAGGTCCTATCCCT 59.139 55.000 0.00 0.00 32.86 4.20
3052 3406 1.162698 GTGGTTTTAACGGAGGGAGC 58.837 55.000 0.00 0.00 0.00 4.70
3091 3445 4.882427 GGTTCAAGCTAAAAGATACTCCCC 59.118 45.833 0.00 0.00 0.00 4.81
3189 3544 1.227409 GCTAGGGAAAGGCTCTCGC 60.227 63.158 0.00 0.00 0.00 5.03
3222 3595 7.585286 TTTATCTTTTGCTTGCAAATGCTAG 57.415 32.000 19.46 14.16 44.65 3.42
3263 3636 4.891756 AGGCTTGCTATATTGATGCAAAGT 59.108 37.500 0.00 0.00 44.49 2.66
3380 3753 1.068264 GCAGCTACCAGCAAAAGGAAC 60.068 52.381 0.38 0.00 45.56 3.62
3809 4203 4.699637 TCACACTCAACGGACAGTATTTT 58.300 39.130 0.00 0.00 0.00 1.82
3881 4275 4.363999 GTCTCCTCCACAAGATTCATACG 58.636 47.826 0.00 0.00 0.00 3.06
4106 4500 9.716556 ATAGATATTAGATTGAGGATAACGGGT 57.283 33.333 0.00 0.00 0.00 5.28
4430 4826 6.306987 AGTTATGGACAGTCAAAGGAAACAT 58.693 36.000 2.17 0.00 0.00 2.71
4858 5256 5.568023 CGAAGTATCTTTAAGTGTGGGGTCA 60.568 44.000 0.00 0.00 0.00 4.02
5062 5460 9.753669 CACCATTTTCAAAACTTCAAGTAAAAC 57.246 29.630 0.00 0.00 0.00 2.43
5063 5461 9.712305 TCACCATTTTCAAAACTTCAAGTAAAA 57.288 25.926 0.00 0.00 0.00 1.52
5079 5505 9.921637 TTGTAACATTCCTATTTCACCATTTTC 57.078 29.630 0.00 0.00 0.00 2.29
5099 5525 6.414694 CCACATGAATTATCGTGCATTGTAAC 59.585 38.462 0.00 0.00 44.87 2.50
5123 5549 7.857885 CAGCTTTTATTTCGATGTTAAGATCCC 59.142 37.037 7.00 0.00 0.00 3.85
5133 5559 9.390795 CAAATATCTCCAGCTTTTATTTCGATG 57.609 33.333 0.00 0.00 0.00 3.84
5325 5905 5.163581 CCATGAATGTGAATTGAGTCTTCCC 60.164 44.000 0.00 0.00 0.00 3.97
5401 5985 1.072331 CACCACTCCTGCCAGTTACTT 59.928 52.381 0.00 0.00 0.00 2.24
5419 6003 1.640428 TCGTCTCAATGAATCGGCAC 58.360 50.000 6.83 0.00 0.00 5.01
5461 6046 2.226437 AGTAAAAATGCCACAGACGCTG 59.774 45.455 5.47 5.47 37.52 5.18
5499 6085 4.366684 GGCCTCCCCTTGTGGTGG 62.367 72.222 0.00 0.00 41.15 4.61
5518 6104 2.004733 TGCAGTTCATGAATCTCAGCG 58.995 47.619 12.12 1.09 0.00 5.18
5584 6170 0.179111 CGCTCCTGCCGATTACTCAA 60.179 55.000 0.00 0.00 35.36 3.02
5671 6258 0.104487 TACGGTGCTCGGTTGTTTCA 59.896 50.000 4.24 0.00 44.45 2.69
5688 6275 3.810188 GGCCTGGCCTTCCCCTAC 61.810 72.222 30.42 0.00 46.69 3.18
5766 6353 8.804912 AGTTTCGTCTTAATAGAGGACTAAGA 57.195 34.615 0.00 0.00 43.05 2.10
5819 6406 2.028294 TGCGGAAACTCGGGTAAACATA 60.028 45.455 0.00 0.00 0.00 2.29
5880 6467 9.241317 GAAATCAGCATGTTTATGGAAATACAG 57.759 33.333 0.00 0.00 37.40 2.74
5885 6472 9.806203 CTATTGAAATCAGCATGTTTATGGAAA 57.194 29.630 0.00 0.00 37.40 3.13
5926 6516 7.872993 TGCTGACTTAATATGAATAGGTAGTGC 59.127 37.037 0.00 0.00 0.00 4.40
5931 6521 9.905713 TTTCTTGCTGACTTAATATGAATAGGT 57.094 29.630 0.00 0.00 0.00 3.08
5964 6554 5.045942 ACAGTACCAACATATCCATGTGTGA 60.046 40.000 0.00 0.00 44.83 3.58
5965 6555 5.185454 ACAGTACCAACATATCCATGTGTG 58.815 41.667 0.00 0.00 44.83 3.82
5966 6556 5.435686 ACAGTACCAACATATCCATGTGT 57.564 39.130 0.00 0.00 44.83 3.72
5967 6557 6.427853 CCATACAGTACCAACATATCCATGTG 59.572 42.308 0.00 0.00 44.83 3.21
5969 6559 6.533730 ACCATACAGTACCAACATATCCATG 58.466 40.000 0.00 0.00 38.21 3.66
5970 6560 6.763715 ACCATACAGTACCAACATATCCAT 57.236 37.500 0.00 0.00 0.00 3.41
5971 6561 6.569127 AACCATACAGTACCAACATATCCA 57.431 37.500 0.00 0.00 0.00 3.41
5972 6562 6.238648 GCAAACCATACAGTACCAACATATCC 60.239 42.308 0.00 0.00 0.00 2.59
5973 6563 6.542370 AGCAAACCATACAGTACCAACATATC 59.458 38.462 0.00 0.00 0.00 1.63
5974 6564 6.423182 AGCAAACCATACAGTACCAACATAT 58.577 36.000 0.00 0.00 0.00 1.78
5975 6565 5.811190 AGCAAACCATACAGTACCAACATA 58.189 37.500 0.00 0.00 0.00 2.29
5976 6566 4.662278 AGCAAACCATACAGTACCAACAT 58.338 39.130 0.00 0.00 0.00 2.71
5977 6567 4.069304 GAGCAAACCATACAGTACCAACA 58.931 43.478 0.00 0.00 0.00 3.33
5978 6568 4.324267 AGAGCAAACCATACAGTACCAAC 58.676 43.478 0.00 0.00 0.00 3.77
5979 6569 4.634012 AGAGCAAACCATACAGTACCAA 57.366 40.909 0.00 0.00 0.00 3.67
5980 6570 4.634012 AAGAGCAAACCATACAGTACCA 57.366 40.909 0.00 0.00 0.00 3.25
5981 6571 5.705905 AGAAAAGAGCAAACCATACAGTACC 59.294 40.000 0.00 0.00 0.00 3.34
5982 6572 6.803154 AGAAAAGAGCAAACCATACAGTAC 57.197 37.500 0.00 0.00 0.00 2.73
5984 6574 9.686683 ATAATAGAAAAGAGCAAACCATACAGT 57.313 29.630 0.00 0.00 0.00 3.55
6332 6971 7.676004 TGTGAACATGTTCTAGAAACTCCATA 58.324 34.615 32.57 10.54 40.14 2.74
6661 7302 3.505680 CCTGTGCCAAGTAAAGTATGCAA 59.494 43.478 0.00 0.00 0.00 4.08
6703 7344 3.055385 CGATGGATTACCGACCCCAATAT 60.055 47.826 0.00 0.00 39.42 1.28
6710 7351 0.600255 CCAGCGATGGATTACCGACC 60.600 60.000 16.48 0.00 39.42 4.79
6854 7503 4.273148 GTGAGAACACATACAAGAGGGT 57.727 45.455 0.00 0.00 45.32 4.34
6879 7529 5.963865 ACTGCCTTTAAATTACCATGGGATT 59.036 36.000 18.09 12.89 0.00 3.01
6889 7539 5.001232 ACTGAAGCGACTGCCTTTAAATTA 58.999 37.500 0.00 0.00 44.31 1.40
6893 7543 2.224185 TGACTGAAGCGACTGCCTTTAA 60.224 45.455 0.00 0.00 44.31 1.52
6896 7546 0.106708 TTGACTGAAGCGACTGCCTT 59.893 50.000 0.00 0.00 44.31 4.35
6911 7561 0.676466 TGTGGGCGTGATGGATTGAC 60.676 55.000 0.00 0.00 0.00 3.18
6912 7562 0.676466 GTGTGGGCGTGATGGATTGA 60.676 55.000 0.00 0.00 0.00 2.57
7059 7720 2.492088 GGGGCAACTCTTGTTTACCATC 59.508 50.000 0.00 0.00 33.63 3.51
7119 7780 1.444933 TGACCATGGAAGTGGAAGGT 58.555 50.000 21.47 0.00 42.02 3.50
7156 7819 1.421382 AAACATAACGACACGTCCCG 58.579 50.000 4.75 4.75 39.99 5.14
7158 7821 2.545106 ACCAAAACATAACGACACGTCC 59.455 45.455 0.00 0.00 39.99 4.79
7318 7982 9.620660 GTATTTTTCGTATTCCTGTGTTTTGAT 57.379 29.630 0.00 0.00 0.00 2.57
7326 7990 8.405531 CCAATCATGTATTTTTCGTATTCCTGT 58.594 33.333 0.00 0.00 0.00 4.00
7375 8043 7.703621 CAGAACATTTGGTTTGCTAATCCTATG 59.296 37.037 0.00 0.00 40.63 2.23
7397 8065 6.984474 GGTATCGAACAATCTATGGTTCAGAA 59.016 38.462 10.15 0.00 42.67 3.02
7398 8066 6.097696 TGGTATCGAACAATCTATGGTTCAGA 59.902 38.462 10.15 8.41 42.67 3.27
7399 8067 6.280643 TGGTATCGAACAATCTATGGTTCAG 58.719 40.000 10.15 4.21 42.67 3.02
7400 8068 6.228616 TGGTATCGAACAATCTATGGTTCA 57.771 37.500 10.15 0.00 42.67 3.18
7401 8069 8.304596 TCTATGGTATCGAACAATCTATGGTTC 58.695 37.037 0.00 0.78 39.92 3.62
7402 8070 8.190326 TCTATGGTATCGAACAATCTATGGTT 57.810 34.615 0.00 0.00 0.00 3.67
7404 8072 9.489084 TTTTCTATGGTATCGAACAATCTATGG 57.511 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.