Multiple sequence alignment - TraesCS6A01G142600

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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 TraesCS6A01G142600 chr6A 100.000 3865 0 0 1 3865 117415698 117411834 0.000000e+00 7138
1 TraesCS6A01G142600 chr6A 100.000 121 0 0 4175 4295 117411524 117411404 1.550000e-54 224
2 TraesCS6A01G142600 chr6B 95.590 3333 105 11 479 3800 183335134 183331833 0.000000e+00 5302
3 TraesCS6A01G142600 chr6B 93.333 450 24 2 1 449 183337140 183336696 0.000000e+00 660
4 TraesCS6A01G142600 chr6B 81.306 444 58 11 1 428 698040664 698040230 1.910000e-88 337
5 TraesCS6A01G142600 chr6D 96.154 3250 82 19 611 3846 98130501 98127281 0.000000e+00 5269
6 TraesCS6A01G142600 chr6D 93.610 626 19 8 1 608 98133026 98132404 0.000000e+00 915
7 TraesCS6A01G142600 chrUn 89.809 1521 122 15 2356 3865 308088296 308089794 0.000000e+00 1919
8 TraesCS6A01G142600 chrUn 86.394 1639 145 36 755 2362 308086280 308087871 0.000000e+00 1720
9 TraesCS6A01G142600 chrUn 82.957 575 42 33 755 1306 432033607 432034148 6.500000e-128 468
10 TraesCS6A01G142600 chrUn 74.834 453 50 29 261 658 432032999 432033442 3.460000e-31 147
11 TraesCS6A01G142600 chr4A 89.809 1521 122 15 2356 3865 592546139 592547637 0.000000e+00 1919
12 TraesCS6A01G142600 chr4A 89.678 1521 125 14 2356 3865 593114948 593116447 0.000000e+00 1910
13 TraesCS6A01G142600 chr4A 86.801 1682 144 35 712 2362 593112889 593114523 0.000000e+00 1805
14 TraesCS6A01G142600 chr4A 86.774 1671 143 34 723 2362 591499470 591497847 0.000000e+00 1790
15 TraesCS6A01G142600 chr4A 86.699 1639 140 36 755 2362 592830050 592831641 0.000000e+00 1748
16 TraesCS6A01G142600 chr4A 86.394 1639 145 36 755 2362 592544123 592545714 0.000000e+00 1720
17 TraesCS6A01G142600 chr4A 91.693 626 48 3 2356 2979 591497425 591496802 0.000000e+00 865
18 TraesCS6A01G142600 chr4A 90.083 121 8 4 4175 4294 656901749 656901632 2.070000e-33 154
19 TraesCS6A01G142600 chr4A 75.000 452 50 29 261 658 593111881 593112323 2.680000e-32 150
20 TraesCS6A01G142600 chr4A 74.834 453 50 29 261 658 592543512 592543955 3.460000e-31 147
21 TraesCS6A01G142600 chr4A 74.834 453 50 29 261 658 592829442 592829885 3.460000e-31 147
22 TraesCS6A01G142600 chr4A 74.779 452 51 29 261 658 591500383 591499941 1.240000e-30 145
23 TraesCS6A01G142600 chr4B 89.817 1473 115 15 2407 3865 20279712 20278261 0.000000e+00 1857
24 TraesCS6A01G142600 chr4B 89.735 1169 110 8 1118 2278 20280908 20279742 0.000000e+00 1485
25 TraesCS6A01G142600 chr4B 79.263 868 94 38 260 1079 20281734 20280905 1.060000e-145 527
26 TraesCS6A01G142600 chr4B 95.192 104 4 1 4175 4277 30854639 30854742 3.440000e-36 163
27 TraesCS6A01G142600 chr4D 90.365 1370 111 9 2407 3765 10766286 10764927 0.000000e+00 1779
28 TraesCS6A01G142600 chr4D 89.227 1216 109 13 1081 2278 10767527 10766316 0.000000e+00 1500
29 TraesCS6A01G142600 chr4D 86.695 466 22 20 609 1063 10768013 10767577 8.350000e-132 481
30 TraesCS6A01G142600 chr7B 79.101 890 178 8 2444 3329 517625125 517626010 1.320000e-169 606
31 TraesCS6A01G142600 chr7B 98.980 98 1 0 4175 4272 697083862 697083959 4.410000e-40 176
32 TraesCS6A01G142600 chr7A 100.000 121 0 0 4175 4295 19961086 19960966 1.550000e-54 224
33 TraesCS6A01G142600 chr7A 96.117 103 3 1 4175 4276 721562761 721562863 2.660000e-37 167
34 TraesCS6A01G142600 chr7A 95.192 104 4 1 4175 4277 681575371 681575474 3.440000e-36 163
35 TraesCS6A01G142600 chr3B 96.154 104 3 1 4175 4277 762628858 762628961 7.390000e-38 169
36 TraesCS6A01G142600 chr1B 96.154 104 3 1 4175 4277 441997585 441997482 7.390000e-38 169
37 TraesCS6A01G142600 chr3A 95.192 104 4 1 4175 4277 625234478 625234375 3.440000e-36 163


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 TraesCS6A01G142600 chr6A 117411404 117415698 4294 True 3681.000000 7138 100.000000 1 4295 2 chr6A.!!$R1 4294
1 TraesCS6A01G142600 chr6B 183331833 183337140 5307 True 2981.000000 5302 94.461500 1 3800 2 chr6B.!!$R2 3799
2 TraesCS6A01G142600 chr6D 98127281 98133026 5745 True 3092.000000 5269 94.882000 1 3846 2 chr6D.!!$R1 3845
3 TraesCS6A01G142600 chrUn 308086280 308089794 3514 False 1819.500000 1919 88.101500 755 3865 2 chrUn.!!$F1 3110
4 TraesCS6A01G142600 chrUn 432032999 432034148 1149 False 307.500000 468 78.895500 261 1306 2 chrUn.!!$F2 1045
5 TraesCS6A01G142600 chr4A 593111881 593116447 4566 False 1288.333333 1910 83.826333 261 3865 3 chr4A.!!$F3 3604
6 TraesCS6A01G142600 chr4A 592543512 592547637 4125 False 1262.000000 1919 83.679000 261 3865 3 chr4A.!!$F1 3604
7 TraesCS6A01G142600 chr4A 592829442 592831641 2199 False 947.500000 1748 80.766500 261 2362 2 chr4A.!!$F2 2101
8 TraesCS6A01G142600 chr4A 591496802 591500383 3581 True 933.333333 1790 84.415333 261 2979 3 chr4A.!!$R2 2718
9 TraesCS6A01G142600 chr4B 20278261 20281734 3473 True 1289.666667 1857 86.271667 260 3865 3 chr4B.!!$R1 3605
10 TraesCS6A01G142600 chr4D 10764927 10768013 3086 True 1253.333333 1779 88.762333 609 3765 3 chr4D.!!$R1 3156
11 TraesCS6A01G142600 chr7B 517625125 517626010 885 False 606.000000 606 79.101000 2444 3329 1 chr7B.!!$F1 885

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
506 2050 1.476007 GCTCTGCCCCTCCGACATAT 61.476 60.0 0.00 0.00 0.00 1.78 F
1188 5266 0.604780 ATATCCTGGCACTGCGATGC 60.605 55.0 3.45 3.45 45.34 3.91 F
2008 6118 1.133809 TGACCTTGGGCCTAGCAGTT 61.134 55.0 9.68 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 5455 0.809241 CTCCTGAGATGCGTTGAGGC 60.809 60.000 0.0 0.0 0.0 4.70 R
2147 6257 1.134580 AGCTGATGATGACGAACTGGG 60.135 52.381 0.0 0.0 0.0 4.45 R
3342 7885 0.314935 AAGCCATCTTTGTTGCGGTG 59.685 50.000 0.0 0.0 0.0 4.94 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
40 41 7.809331 TGAGAATTATCATGAGCACAAACAAAC 59.191 33.333 0.09 0.00 0.00 2.93
104 105 7.626084 TCCTCTAGGTTGTATTTGGGAGAATTA 59.374 37.037 0.00 0.00 36.34 1.40
120 121 9.268282 TGGGAGAATTAAGTAACAAGATAGACT 57.732 33.333 0.00 0.00 0.00 3.24
193 194 3.921677 TCACCAACCAGATCGTAACTTC 58.078 45.455 0.00 0.00 0.00 3.01
331 333 2.809601 GCCTACACACGTGCTCCG 60.810 66.667 17.22 4.30 44.03 4.63
506 2050 1.476007 GCTCTGCCCCTCCGACATAT 61.476 60.000 0.00 0.00 0.00 1.78
799 4803 7.497909 TCGAACCCTTTAATCATAGTTCAATCC 59.502 37.037 0.00 0.00 34.65 3.01
871 4882 5.650543 GTGCCACCTTTTTACCATATCTTG 58.349 41.667 0.00 0.00 0.00 3.02
1006 5043 3.153369 TCTTGTAAGCAGCCATGGAAA 57.847 42.857 18.40 0.00 0.00 3.13
1188 5266 0.604780 ATATCCTGGCACTGCGATGC 60.605 55.000 3.45 3.45 45.34 3.91
1205 5283 3.462021 GATGCAGGATGTAGGTTCAGAC 58.538 50.000 0.00 0.00 39.31 3.51
1213 5291 2.867624 TGTAGGTTCAGACTACACCGT 58.132 47.619 1.48 0.00 44.14 4.83
1364 5455 4.307432 TCTTCTCTTTTTACTGCTGACCG 58.693 43.478 0.00 0.00 0.00 4.79
1382 5477 1.219124 GCCTCAACGCATCTCAGGA 59.781 57.895 0.00 0.00 0.00 3.86
1539 5635 2.557452 CCACTTATTGGGGCCTTCTTGT 60.557 50.000 0.84 0.00 42.54 3.16
1643 5752 3.119101 ACCGACCAGATCTGTATGACAAC 60.119 47.826 21.11 3.09 0.00 3.32
1644 5753 3.119137 CCGACCAGATCTGTATGACAACA 60.119 47.826 21.11 0.00 0.00 3.33
1645 5754 4.494484 CGACCAGATCTGTATGACAACAA 58.506 43.478 21.11 0.00 0.00 2.83
1708 5818 1.197036 CTCACAGTTGCAGCATCAGTG 59.803 52.381 18.44 18.44 0.00 3.66
1717 5827 4.206958 GCATCAGTGCCGACATCA 57.793 55.556 0.00 0.00 45.76 3.07
1726 5836 2.764010 AGTGCCGACATCATACTACCAA 59.236 45.455 0.00 0.00 0.00 3.67
1734 5844 4.708177 ACATCATACTACCAAGGTGATGC 58.292 43.478 13.49 0.00 44.96 3.91
1894 6004 6.436532 CCTTCTTCAACTGGTACTACTTCCTA 59.563 42.308 0.00 0.00 0.00 2.94
2008 6118 1.133809 TGACCTTGGGCCTAGCAGTT 61.134 55.000 9.68 0.00 0.00 3.16
2071 6181 2.434336 AGCAAGCCCATTCACGAGTATA 59.566 45.455 0.00 0.00 0.00 1.47
2140 6250 5.394005 GCCAGATGATATCTCGCTCTTGTAT 60.394 44.000 3.98 0.00 39.90 2.29
2341 6451 3.691118 TGAGCTGTGACATCTTATTTGCC 59.309 43.478 0.00 0.00 0.00 4.52
2399 6941 7.339212 ACCATATCTAGAGACTGCATCTATGAC 59.661 40.741 0.00 0.00 38.00 3.06
2413 6956 8.504812 TGCATCTATGACTAAACTTAAATGCA 57.495 30.769 0.00 0.00 42.27 3.96
2510 7053 2.901042 GCCCCCGTTAGACCAGAG 59.099 66.667 0.00 0.00 0.00 3.35
2584 7127 6.382570 AGTTGAGGAGTTGAAGATACTGCTAT 59.617 38.462 0.00 0.00 43.23 2.97
2951 7494 0.251474 AATGTGCCTGTGCCAGTGAT 60.251 50.000 0.00 0.00 36.33 3.06
3118 7661 0.319555 AGCTTACTTCAACGCGCTCA 60.320 50.000 5.73 0.00 0.00 4.26
3231 7774 2.104451 CTGGATGATGGCTGCTCTTAGT 59.896 50.000 0.00 0.00 0.00 2.24
3342 7885 4.079730 AGGATTAAAGACTTCCCCCATCAC 60.080 45.833 0.00 0.00 0.00 3.06
3420 7968 8.267183 TGCTTCCATCGGAATGATACATAATAT 58.733 33.333 0.00 0.00 41.23 1.28
3421 7969 8.554528 GCTTCCATCGGAATGATACATAATATG 58.445 37.037 0.00 0.00 41.23 1.78
3424 7972 6.767423 CCATCGGAATGATACATAATATGCCA 59.233 38.462 0.00 0.00 34.83 4.92
3639 8205 4.231718 TCAAAGTGGTATTTTTCACGCC 57.768 40.909 0.00 0.00 38.77 5.68
3641 8207 4.098044 TCAAAGTGGTATTTTTCACGCCAA 59.902 37.500 0.00 0.00 38.77 4.52
3642 8208 4.657436 AAGTGGTATTTTTCACGCCAAA 57.343 36.364 0.00 0.00 38.77 3.28
3643 8209 4.657436 AGTGGTATTTTTCACGCCAAAA 57.343 36.364 0.00 0.00 38.77 2.44
3644 8210 5.012328 AGTGGTATTTTTCACGCCAAAAA 57.988 34.783 7.16 7.16 39.09 1.94
3672 8238 5.791336 AGAAAAGAATCCCAAGTGGTTTC 57.209 39.130 0.00 0.00 41.38 2.78
4191 8764 3.330720 CCGGGCTCTCAACCCCTT 61.331 66.667 0.00 0.00 45.37 3.95
4192 8765 2.757077 CGGGCTCTCAACCCCTTT 59.243 61.111 0.00 0.00 45.37 3.11
4193 8766 1.377333 CGGGCTCTCAACCCCTTTC 60.377 63.158 0.00 0.00 45.37 2.62
4194 8767 1.000771 GGGCTCTCAACCCCTTTCC 60.001 63.158 0.00 0.00 42.01 3.13
4195 8768 1.767692 GGCTCTCAACCCCTTTCCA 59.232 57.895 0.00 0.00 0.00 3.53
4196 8769 0.332972 GGCTCTCAACCCCTTTCCAT 59.667 55.000 0.00 0.00 0.00 3.41
4197 8770 1.272704 GGCTCTCAACCCCTTTCCATT 60.273 52.381 0.00 0.00 0.00 3.16
4198 8771 2.025321 GGCTCTCAACCCCTTTCCATTA 60.025 50.000 0.00 0.00 0.00 1.90
4199 8772 3.563479 GGCTCTCAACCCCTTTCCATTAA 60.563 47.826 0.00 0.00 0.00 1.40
4200 8773 4.281657 GCTCTCAACCCCTTTCCATTAAT 58.718 43.478 0.00 0.00 0.00 1.40
4201 8774 4.711846 GCTCTCAACCCCTTTCCATTAATT 59.288 41.667 0.00 0.00 0.00 1.40
4202 8775 5.187772 GCTCTCAACCCCTTTCCATTAATTT 59.812 40.000 0.00 0.00 0.00 1.82
4203 8776 6.628175 GCTCTCAACCCCTTTCCATTAATTTC 60.628 42.308 0.00 0.00 0.00 2.17
4204 8777 5.417580 TCTCAACCCCTTTCCATTAATTTCG 59.582 40.000 0.00 0.00 0.00 3.46
4205 8778 4.081917 TCAACCCCTTTCCATTAATTTCGC 60.082 41.667 0.00 0.00 0.00 4.70
4206 8779 3.436243 ACCCCTTTCCATTAATTTCGCA 58.564 40.909 0.00 0.00 0.00 5.10
4207 8780 3.835395 ACCCCTTTCCATTAATTTCGCAA 59.165 39.130 0.00 0.00 0.00 4.85
4208 8781 4.469586 ACCCCTTTCCATTAATTTCGCAAT 59.530 37.500 0.00 0.00 0.00 3.56
4209 8782 5.049828 CCCCTTTCCATTAATTTCGCAATC 58.950 41.667 0.00 0.00 0.00 2.67
4210 8783 5.395103 CCCCTTTCCATTAATTTCGCAATCA 60.395 40.000 0.00 0.00 0.00 2.57
4211 8784 6.105333 CCCTTTCCATTAATTTCGCAATCAA 58.895 36.000 0.00 0.00 0.00 2.57
4212 8785 6.035975 CCCTTTCCATTAATTTCGCAATCAAC 59.964 38.462 0.00 0.00 0.00 3.18
4213 8786 6.237542 CCTTTCCATTAATTTCGCAATCAACG 60.238 38.462 0.00 0.00 0.00 4.10
4214 8787 4.667262 TCCATTAATTTCGCAATCAACGG 58.333 39.130 0.00 0.00 0.00 4.44
4215 8788 4.396478 TCCATTAATTTCGCAATCAACGGA 59.604 37.500 0.00 0.00 0.00 4.69
4216 8789 5.098893 CCATTAATTTCGCAATCAACGGAA 58.901 37.500 0.00 0.00 31.46 4.30
4217 8790 5.574830 CCATTAATTTCGCAATCAACGGAAA 59.425 36.000 0.00 0.00 30.52 3.13
4218 8791 6.255453 CCATTAATTTCGCAATCAACGGAAAT 59.745 34.615 0.00 0.00 30.52 2.17
4219 8792 7.433719 CCATTAATTTCGCAATCAACGGAAATA 59.566 33.333 0.00 0.00 30.52 1.40
4220 8793 7.728580 TTAATTTCGCAATCAACGGAAATAC 57.271 32.000 0.00 0.00 30.52 1.89
4221 8794 4.750952 TTTCGCAATCAACGGAAATACA 57.249 36.364 0.00 0.00 0.00 2.29
4222 8795 4.955925 TTCGCAATCAACGGAAATACAT 57.044 36.364 0.00 0.00 0.00 2.29
4223 8796 4.530094 TCGCAATCAACGGAAATACATC 57.470 40.909 0.00 0.00 0.00 3.06
4224 8797 3.935828 TCGCAATCAACGGAAATACATCA 59.064 39.130 0.00 0.00 0.00 3.07
4225 8798 4.033932 TCGCAATCAACGGAAATACATCAG 59.966 41.667 0.00 0.00 0.00 2.90
4226 8799 4.201812 CGCAATCAACGGAAATACATCAGT 60.202 41.667 0.00 0.00 0.00 3.41
4227 8800 5.266242 GCAATCAACGGAAATACATCAGTC 58.734 41.667 0.00 0.00 0.00 3.51
4228 8801 5.065218 GCAATCAACGGAAATACATCAGTCT 59.935 40.000 0.00 0.00 0.00 3.24
4229 8802 6.481134 CAATCAACGGAAATACATCAGTCTG 58.519 40.000 0.00 0.00 0.00 3.51
4230 8803 5.147330 TCAACGGAAATACATCAGTCTGT 57.853 39.130 0.00 0.00 0.00 3.41
4231 8804 6.275494 TCAACGGAAATACATCAGTCTGTA 57.725 37.500 0.00 0.00 36.14 2.74
4232 8805 6.873997 TCAACGGAAATACATCAGTCTGTAT 58.126 36.000 0.00 0.00 42.68 2.29
4233 8806 6.978659 TCAACGGAAATACATCAGTCTGTATC 59.021 38.462 0.00 0.00 40.57 2.24
4234 8807 5.844004 ACGGAAATACATCAGTCTGTATCC 58.156 41.667 0.00 0.00 40.57 2.59
4235 8808 5.362717 ACGGAAATACATCAGTCTGTATCCA 59.637 40.000 0.00 0.00 40.57 3.41
4236 8809 5.923114 CGGAAATACATCAGTCTGTATCCAG 59.077 44.000 0.00 0.00 40.57 3.86
4237 8810 6.239036 CGGAAATACATCAGTCTGTATCCAGA 60.239 42.308 0.00 0.00 45.44 3.86
4251 8824 8.008513 TCTGTATCCAGATGTTCTTAGTAACC 57.991 38.462 0.00 0.00 42.80 2.85
4252 8825 7.618117 TCTGTATCCAGATGTTCTTAGTAACCA 59.382 37.037 0.00 0.00 42.80 3.67
4253 8826 8.141298 TGTATCCAGATGTTCTTAGTAACCAA 57.859 34.615 0.00 0.00 0.00 3.67
4254 8827 8.038944 TGTATCCAGATGTTCTTAGTAACCAAC 58.961 37.037 0.00 0.00 0.00 3.77
4255 8828 5.801380 TCCAGATGTTCTTAGTAACCAACC 58.199 41.667 0.00 0.00 0.00 3.77
4256 8829 5.308497 TCCAGATGTTCTTAGTAACCAACCA 59.692 40.000 0.00 0.00 0.00 3.67
4257 8830 5.411669 CCAGATGTTCTTAGTAACCAACCAC 59.588 44.000 0.00 0.00 0.00 4.16
4258 8831 6.231211 CAGATGTTCTTAGTAACCAACCACT 58.769 40.000 0.00 0.00 0.00 4.00
4259 8832 7.383687 CAGATGTTCTTAGTAACCAACCACTA 58.616 38.462 0.00 0.00 0.00 2.74
4260 8833 7.331193 CAGATGTTCTTAGTAACCAACCACTAC 59.669 40.741 0.00 0.00 0.00 2.73
4261 8834 6.482898 TGTTCTTAGTAACCAACCACTACA 57.517 37.500 0.00 0.00 0.00 2.74
4262 8835 6.887013 TGTTCTTAGTAACCAACCACTACAA 58.113 36.000 0.00 0.00 0.00 2.41
4263 8836 6.762661 TGTTCTTAGTAACCAACCACTACAAC 59.237 38.462 0.00 0.00 0.00 3.32
4264 8837 6.736110 TCTTAGTAACCAACCACTACAACT 57.264 37.500 0.00 0.00 0.00 3.16
4265 8838 7.838079 TCTTAGTAACCAACCACTACAACTA 57.162 36.000 0.00 0.00 0.00 2.24
4266 8839 7.889469 TCTTAGTAACCAACCACTACAACTAG 58.111 38.462 0.00 0.00 0.00 2.57
4267 8840 4.891260 AGTAACCAACCACTACAACTAGC 58.109 43.478 0.00 0.00 0.00 3.42
4268 8841 3.849563 AACCAACCACTACAACTAGCA 57.150 42.857 0.00 0.00 0.00 3.49
4269 8842 3.402628 ACCAACCACTACAACTAGCAG 57.597 47.619 0.00 0.00 0.00 4.24
4270 8843 2.038557 ACCAACCACTACAACTAGCAGG 59.961 50.000 0.00 0.00 0.00 4.85
4271 8844 2.301870 CCAACCACTACAACTAGCAGGA 59.698 50.000 0.00 0.00 0.00 3.86
4272 8845 3.055094 CCAACCACTACAACTAGCAGGAT 60.055 47.826 0.00 0.00 0.00 3.24
4273 8846 3.895232 ACCACTACAACTAGCAGGATG 57.105 47.619 0.00 0.00 40.87 3.51
4274 8847 3.441101 ACCACTACAACTAGCAGGATGA 58.559 45.455 0.00 0.00 39.69 2.92
4275 8848 3.838317 ACCACTACAACTAGCAGGATGAA 59.162 43.478 0.00 0.00 39.69 2.57
4276 8849 4.286032 ACCACTACAACTAGCAGGATGAAA 59.714 41.667 0.00 0.00 39.69 2.69
4277 8850 5.221843 ACCACTACAACTAGCAGGATGAAAA 60.222 40.000 0.00 0.00 39.69 2.29
4278 8851 5.705441 CCACTACAACTAGCAGGATGAAAAA 59.295 40.000 0.00 0.00 39.69 1.94
4279 8852 6.348540 CCACTACAACTAGCAGGATGAAAAAC 60.349 42.308 0.00 0.00 39.69 2.43
4280 8853 6.204688 CACTACAACTAGCAGGATGAAAAACA 59.795 38.462 0.00 0.00 39.69 2.83
4281 8854 5.438761 ACAACTAGCAGGATGAAAAACAC 57.561 39.130 0.00 0.00 39.69 3.32
4282 8855 4.887071 ACAACTAGCAGGATGAAAAACACA 59.113 37.500 0.00 0.00 39.69 3.72
4283 8856 5.359576 ACAACTAGCAGGATGAAAAACACAA 59.640 36.000 0.00 0.00 39.69 3.33
4284 8857 6.127479 ACAACTAGCAGGATGAAAAACACAAA 60.127 34.615 0.00 0.00 39.69 2.83
4285 8858 6.463995 ACTAGCAGGATGAAAAACACAAAA 57.536 33.333 0.00 0.00 39.69 2.44
4286 8859 6.507023 ACTAGCAGGATGAAAAACACAAAAG 58.493 36.000 0.00 0.00 39.69 2.27
4287 8860 4.122046 AGCAGGATGAAAAACACAAAAGC 58.878 39.130 0.00 0.00 39.69 3.51
4288 8861 3.248363 GCAGGATGAAAAACACAAAAGCC 59.752 43.478 0.00 0.00 39.69 4.35
4289 8862 4.696455 CAGGATGAAAAACACAAAAGCCT 58.304 39.130 0.00 0.00 39.69 4.58
4290 8863 5.118286 CAGGATGAAAAACACAAAAGCCTT 58.882 37.500 0.00 0.00 39.69 4.35
4291 8864 5.006941 CAGGATGAAAAACACAAAAGCCTTG 59.993 40.000 0.00 0.00 39.69 3.61
4292 8865 5.104982 AGGATGAAAAACACAAAAGCCTTGA 60.105 36.000 3.27 0.00 0.00 3.02
4293 8866 5.234972 GGATGAAAAACACAAAAGCCTTGAG 59.765 40.000 3.27 0.00 0.00 3.02
4294 8867 5.398603 TGAAAAACACAAAAGCCTTGAGA 57.601 34.783 3.27 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 7.175119 ACAACCTAGAGGAGAAATTTGCTTAAC 59.825 37.037 1.60 0.00 38.94 2.01
85 86 9.016438 TGTTACTTAATTCTCCCAAATACAACC 57.984 33.333 0.00 0.00 0.00 3.77
120 121 7.094420 GCTAGTGCTTCTCTCTCACATATGATA 60.094 40.741 10.38 0.00 33.12 2.15
193 194 2.624838 GGCCATCATCACCAAATACCAG 59.375 50.000 0.00 0.00 0.00 4.00
197 198 5.765510 ACTTTAGGCCATCATCACCAAATA 58.234 37.500 5.01 0.00 0.00 1.40
374 383 2.936202 AGCCAACTCTTTTCTGCTTGA 58.064 42.857 0.00 0.00 0.00 3.02
506 2050 2.501723 GTGGCCTACTGAGAGGATTGAA 59.498 50.000 3.32 0.00 39.15 2.69
686 4283 3.535561 CTCTCTCTCTCTCACTCACTCC 58.464 54.545 0.00 0.00 0.00 3.85
799 4803 4.275689 TGTGTTGTGACTGCATTTTCTAGG 59.724 41.667 0.00 0.00 0.00 3.02
871 4882 5.758784 GGTAGGTTGCTTATCAGTTATCACC 59.241 44.000 0.00 0.00 0.00 4.02
1006 5043 2.048409 CTCGTCTGCTGCTGCTGT 60.048 61.111 17.00 0.00 40.48 4.40
1188 5266 4.142138 GGTGTAGTCTGAACCTACATCCTG 60.142 50.000 10.25 0.00 44.67 3.86
1205 5283 1.676529 ACAGATCCATCGACGGTGTAG 59.323 52.381 7.44 0.00 0.00 2.74
1213 5291 4.470334 TTGATGTCAACAGATCCATCGA 57.530 40.909 0.00 0.00 37.18 3.59
1364 5455 0.809241 CTCCTGAGATGCGTTGAGGC 60.809 60.000 0.00 0.00 0.00 4.70
1382 5477 1.073216 CGCATTCGCAGAACTCGACT 61.073 55.000 7.63 0.00 45.90 4.18
1478 5574 3.374402 CAGGCAGAGACGTCCCGT 61.374 66.667 13.01 0.00 45.10 5.28
1484 5580 4.135153 CCGACCCAGGCAGAGACG 62.135 72.222 0.00 0.00 0.00 4.18
1539 5635 6.266330 CAGTATCTTCCCAGATATGTGTCAGA 59.734 42.308 0.00 0.00 42.82 3.27
1643 5752 3.637998 AAGTGTTCAGAGCTGCAATTG 57.362 42.857 1.02 0.00 0.00 2.32
1644 5753 3.633525 TGAAAGTGTTCAGAGCTGCAATT 59.366 39.130 1.02 0.00 38.88 2.32
1645 5754 3.004106 GTGAAAGTGTTCAGAGCTGCAAT 59.996 43.478 1.02 0.00 44.44 3.56
1708 5818 2.102588 ACCTTGGTAGTATGATGTCGGC 59.897 50.000 0.00 0.00 0.00 5.54
1734 5844 1.272490 ACACCACCACAGTACGATGAG 59.728 52.381 0.00 0.00 0.00 2.90
1894 6004 0.827368 GAAGGGAGCCGAGATTGAGT 59.173 55.000 0.00 0.00 0.00 3.41
2071 6181 1.518056 CCGCAACAAGCACCTGACAT 61.518 55.000 0.00 0.00 46.13 3.06
2140 6250 1.830587 ATGACGAACTGGGCAGCTCA 61.831 55.000 0.00 0.00 0.00 4.26
2147 6257 1.134580 AGCTGATGATGACGAACTGGG 60.135 52.381 0.00 0.00 0.00 4.45
2399 6941 8.045176 AGGTAAGCTCTTGCATTTAAGTTTAG 57.955 34.615 0.00 0.00 42.74 1.85
2413 6956 9.649316 ACTTGTAGATATAAGAGGTAAGCTCTT 57.351 33.333 0.00 0.00 42.91 2.85
2510 7053 1.810151 ACAACGGTAACACCATGCATC 59.190 47.619 0.00 0.00 38.47 3.91
2523 7066 1.416401 AGACTCCATGAACACAACGGT 59.584 47.619 0.00 0.00 0.00 4.83
3118 7661 3.119637 GCCACCGCAACAACACTAAATAT 60.120 43.478 0.00 0.00 34.03 1.28
3231 7774 4.022416 ACAAATTGCGCCAGATTCAGTAAA 60.022 37.500 4.18 0.00 0.00 2.01
3342 7885 0.314935 AAGCCATCTTTGTTGCGGTG 59.685 50.000 0.00 0.00 0.00 4.94
3482 8035 2.157738 CTTCTCTTGGCTTGGACTTGG 58.842 52.381 0.00 0.00 0.00 3.61
3593 8159 3.885976 TCCCATCAGTTAACCAAACCA 57.114 42.857 0.88 0.00 39.03 3.67
3594 8160 4.340617 TGATCCCATCAGTTAACCAAACC 58.659 43.478 0.88 0.00 39.03 3.27
3642 8208 7.770433 CCACTTGGGATTCTTTTCTTTCTTTTT 59.230 33.333 0.00 0.00 40.01 1.94
3643 8209 7.092891 ACCACTTGGGATTCTTTTCTTTCTTTT 60.093 33.333 0.00 0.00 41.15 2.27
3644 8210 6.384015 ACCACTTGGGATTCTTTTCTTTCTTT 59.616 34.615 0.00 0.00 41.15 2.52
3645 8211 5.899547 ACCACTTGGGATTCTTTTCTTTCTT 59.100 36.000 0.00 0.00 41.15 2.52
3646 8212 5.458595 ACCACTTGGGATTCTTTTCTTTCT 58.541 37.500 0.00 0.00 41.15 2.52
3647 8213 5.791336 ACCACTTGGGATTCTTTTCTTTC 57.209 39.130 0.00 0.00 41.15 2.62
3736 8304 9.823647 CTGTCCTACAATTGACTATGAAAGTAT 57.176 33.333 13.59 0.00 39.07 2.12
4177 8750 0.332972 ATGGAAAGGGGTTGAGAGCC 59.667 55.000 0.00 0.00 42.86 4.70
4178 8751 2.222227 AATGGAAAGGGGTTGAGAGC 57.778 50.000 0.00 0.00 0.00 4.09
4179 8752 6.404734 CGAAATTAATGGAAAGGGGTTGAGAG 60.405 42.308 0.00 0.00 0.00 3.20
4180 8753 5.417580 CGAAATTAATGGAAAGGGGTTGAGA 59.582 40.000 0.00 0.00 0.00 3.27
4181 8754 5.650543 CGAAATTAATGGAAAGGGGTTGAG 58.349 41.667 0.00 0.00 0.00 3.02
4182 8755 4.081917 GCGAAATTAATGGAAAGGGGTTGA 60.082 41.667 0.00 0.00 0.00 3.18
4183 8756 4.180817 GCGAAATTAATGGAAAGGGGTTG 58.819 43.478 0.00 0.00 0.00 3.77
4184 8757 3.835395 TGCGAAATTAATGGAAAGGGGTT 59.165 39.130 0.00 0.00 0.00 4.11
4185 8758 3.436243 TGCGAAATTAATGGAAAGGGGT 58.564 40.909 0.00 0.00 0.00 4.95
4186 8759 4.464069 TTGCGAAATTAATGGAAAGGGG 57.536 40.909 0.00 0.00 0.00 4.79
4187 8760 5.659463 TGATTGCGAAATTAATGGAAAGGG 58.341 37.500 0.00 0.00 0.00 3.95
4188 8761 6.237542 CGTTGATTGCGAAATTAATGGAAAGG 60.238 38.462 5.17 0.00 0.00 3.11
4189 8762 6.237542 CCGTTGATTGCGAAATTAATGGAAAG 60.238 38.462 22.03 0.48 37.12 2.62
4190 8763 5.574830 CCGTTGATTGCGAAATTAATGGAAA 59.425 36.000 22.03 0.00 37.12 3.13
4191 8764 5.098893 CCGTTGATTGCGAAATTAATGGAA 58.901 37.500 22.03 0.00 37.12 3.53
4192 8765 4.396478 TCCGTTGATTGCGAAATTAATGGA 59.604 37.500 24.13 24.13 39.82 3.41
4193 8766 4.667262 TCCGTTGATTGCGAAATTAATGG 58.333 39.130 20.96 20.96 36.62 3.16
4194 8767 6.624710 TTTCCGTTGATTGCGAAATTAATG 57.375 33.333 5.97 5.97 0.00 1.90
4195 8768 7.971168 TGTATTTCCGTTGATTGCGAAATTAAT 59.029 29.630 0.00 0.00 0.00 1.40
4196 8769 7.306213 TGTATTTCCGTTGATTGCGAAATTAA 58.694 30.769 0.00 0.00 0.00 1.40
4197 8770 6.843208 TGTATTTCCGTTGATTGCGAAATTA 58.157 32.000 0.00 0.00 0.00 1.40
4198 8771 5.704888 TGTATTTCCGTTGATTGCGAAATT 58.295 33.333 0.00 0.00 0.00 1.82
4199 8772 5.303747 TGTATTTCCGTTGATTGCGAAAT 57.696 34.783 0.00 0.00 0.00 2.17
4200 8773 4.750952 TGTATTTCCGTTGATTGCGAAA 57.249 36.364 0.00 0.00 0.00 3.46
4201 8774 4.393371 TGATGTATTTCCGTTGATTGCGAA 59.607 37.500 0.00 0.00 0.00 4.70
4202 8775 3.935828 TGATGTATTTCCGTTGATTGCGA 59.064 39.130 0.00 0.00 0.00 5.10
4203 8776 4.201812 ACTGATGTATTTCCGTTGATTGCG 60.202 41.667 0.00 0.00 0.00 4.85
4204 8777 5.065218 AGACTGATGTATTTCCGTTGATTGC 59.935 40.000 0.00 0.00 0.00 3.56
4205 8778 6.092670 ACAGACTGATGTATTTCCGTTGATTG 59.907 38.462 10.08 0.00 0.00 2.67
4206 8779 6.173339 ACAGACTGATGTATTTCCGTTGATT 58.827 36.000 10.08 0.00 0.00 2.57
4207 8780 5.734720 ACAGACTGATGTATTTCCGTTGAT 58.265 37.500 10.08 0.00 0.00 2.57
4208 8781 5.147330 ACAGACTGATGTATTTCCGTTGA 57.853 39.130 10.08 0.00 0.00 3.18
4209 8782 6.201044 GGATACAGACTGATGTATTTCCGTTG 59.799 42.308 10.08 0.00 44.47 4.10
4210 8783 6.127168 TGGATACAGACTGATGTATTTCCGTT 60.127 38.462 10.08 0.00 44.47 4.44
4211 8784 5.362717 TGGATACAGACTGATGTATTTCCGT 59.637 40.000 10.08 0.00 44.47 4.69
4212 8785 5.842907 TGGATACAGACTGATGTATTTCCG 58.157 41.667 10.08 0.00 44.47 4.30
4229 8802 7.494952 GGTTGGTTACTAAGAACATCTGGATAC 59.505 40.741 0.00 0.00 0.00 2.24
4230 8803 7.181305 TGGTTGGTTACTAAGAACATCTGGATA 59.819 37.037 0.00 0.00 0.00 2.59
4231 8804 6.012858 TGGTTGGTTACTAAGAACATCTGGAT 60.013 38.462 0.00 0.00 0.00 3.41
4232 8805 5.308497 TGGTTGGTTACTAAGAACATCTGGA 59.692 40.000 0.00 0.00 0.00 3.86
4233 8806 5.411669 GTGGTTGGTTACTAAGAACATCTGG 59.588 44.000 0.00 0.00 0.00 3.86
4234 8807 6.231211 AGTGGTTGGTTACTAAGAACATCTG 58.769 40.000 0.00 0.00 0.00 2.90
4235 8808 6.435292 AGTGGTTGGTTACTAAGAACATCT 57.565 37.500 0.00 0.00 0.00 2.90
4236 8809 7.156673 TGTAGTGGTTGGTTACTAAGAACATC 58.843 38.462 0.00 0.00 31.74 3.06
4237 8810 7.069877 TGTAGTGGTTGGTTACTAAGAACAT 57.930 36.000 0.00 0.00 31.74 2.71
4238 8811 6.482898 TGTAGTGGTTGGTTACTAAGAACA 57.517 37.500 0.00 0.00 31.74 3.18
4239 8812 6.988580 AGTTGTAGTGGTTGGTTACTAAGAAC 59.011 38.462 0.00 0.00 31.74 3.01
4240 8813 7.128234 AGTTGTAGTGGTTGGTTACTAAGAA 57.872 36.000 0.00 0.00 31.74 2.52
4241 8814 6.736110 AGTTGTAGTGGTTGGTTACTAAGA 57.264 37.500 0.00 0.00 31.74 2.10
4242 8815 6.589139 GCTAGTTGTAGTGGTTGGTTACTAAG 59.411 42.308 0.00 0.00 31.74 2.18
4243 8816 6.041865 TGCTAGTTGTAGTGGTTGGTTACTAA 59.958 38.462 0.00 0.00 31.74 2.24
4244 8817 5.539574 TGCTAGTTGTAGTGGTTGGTTACTA 59.460 40.000 0.00 0.00 0.00 1.82
4245 8818 4.345837 TGCTAGTTGTAGTGGTTGGTTACT 59.654 41.667 0.00 0.00 0.00 2.24
4246 8819 4.634199 TGCTAGTTGTAGTGGTTGGTTAC 58.366 43.478 0.00 0.00 0.00 2.50
4247 8820 4.262721 CCTGCTAGTTGTAGTGGTTGGTTA 60.263 45.833 0.00 0.00 0.00 2.85
4248 8821 3.496160 CCTGCTAGTTGTAGTGGTTGGTT 60.496 47.826 0.00 0.00 0.00 3.67
4249 8822 2.038557 CCTGCTAGTTGTAGTGGTTGGT 59.961 50.000 0.00 0.00 0.00 3.67
4250 8823 2.301870 TCCTGCTAGTTGTAGTGGTTGG 59.698 50.000 0.00 0.00 0.00 3.77
4251 8824 3.678056 TCCTGCTAGTTGTAGTGGTTG 57.322 47.619 0.00 0.00 0.00 3.77
4252 8825 3.838317 TCATCCTGCTAGTTGTAGTGGTT 59.162 43.478 0.00 0.00 0.00 3.67
4253 8826 3.441101 TCATCCTGCTAGTTGTAGTGGT 58.559 45.455 0.00 0.00 0.00 4.16
4254 8827 4.471904 TTCATCCTGCTAGTTGTAGTGG 57.528 45.455 0.00 0.00 0.00 4.00
4255 8828 6.204688 TGTTTTTCATCCTGCTAGTTGTAGTG 59.795 38.462 0.00 0.00 0.00 2.74
4256 8829 6.204882 GTGTTTTTCATCCTGCTAGTTGTAGT 59.795 38.462 0.00 0.00 0.00 2.73
4257 8830 6.204688 TGTGTTTTTCATCCTGCTAGTTGTAG 59.795 38.462 0.00 0.00 0.00 2.74
4258 8831 6.058833 TGTGTTTTTCATCCTGCTAGTTGTA 58.941 36.000 0.00 0.00 0.00 2.41
4259 8832 4.887071 TGTGTTTTTCATCCTGCTAGTTGT 59.113 37.500 0.00 0.00 0.00 3.32
4260 8833 5.437289 TGTGTTTTTCATCCTGCTAGTTG 57.563 39.130 0.00 0.00 0.00 3.16
4261 8834 6.463995 TTTGTGTTTTTCATCCTGCTAGTT 57.536 33.333 0.00 0.00 0.00 2.24
4262 8835 6.463995 TTTTGTGTTTTTCATCCTGCTAGT 57.536 33.333 0.00 0.00 0.00 2.57
4263 8836 5.403466 GCTTTTGTGTTTTTCATCCTGCTAG 59.597 40.000 0.00 0.00 0.00 3.42
4264 8837 5.288804 GCTTTTGTGTTTTTCATCCTGCTA 58.711 37.500 0.00 0.00 0.00 3.49
4265 8838 4.122046 GCTTTTGTGTTTTTCATCCTGCT 58.878 39.130 0.00 0.00 0.00 4.24
4266 8839 3.248363 GGCTTTTGTGTTTTTCATCCTGC 59.752 43.478 0.00 0.00 0.00 4.85
4267 8840 4.696455 AGGCTTTTGTGTTTTTCATCCTG 58.304 39.130 0.00 0.00 0.00 3.86
4268 8841 5.104982 TCAAGGCTTTTGTGTTTTTCATCCT 60.105 36.000 0.00 0.00 0.00 3.24
4269 8842 5.115480 TCAAGGCTTTTGTGTTTTTCATCC 58.885 37.500 0.00 0.00 0.00 3.51
4270 8843 6.042143 TCTCAAGGCTTTTGTGTTTTTCATC 58.958 36.000 0.00 0.00 0.00 2.92
4271 8844 5.976458 TCTCAAGGCTTTTGTGTTTTTCAT 58.024 33.333 0.00 0.00 0.00 2.57
4272 8845 5.398603 TCTCAAGGCTTTTGTGTTTTTCA 57.601 34.783 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.