Multiple sequence alignment - TraesCS4D01G346900

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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 TraesCS4D01G346900 chr4D 100.000 4093 0 0 1 4093 500719796 500715704 0.000000e+00 7559.0
1 TraesCS4D01G346900 chr4D 89.684 475 46 1 992 1466 502013340 502013811 1.630000e-168 603.0
2 TraesCS4D01G346900 chr4D 78.421 950 125 52 1715 2641 502014261 502015153 2.780000e-151 545.0
3 TraesCS4D01G346900 chr4D 85.294 170 20 4 1516 1681 502013882 502014050 1.960000e-38 171.0
4 TraesCS4D01G346900 chr5A 89.988 3246 181 66 161 3354 683630137 683633290 0.000000e+00 4061.0
5 TraesCS4D01G346900 chr5A 89.770 3255 180 67 161 3354 681900389 681897227 0.000000e+00 4024.0
6 TraesCS4D01G346900 chr5A 79.108 1144 157 55 1516 2641 684647771 684648850 0.000000e+00 713.0
7 TraesCS4D01G346900 chr5A 89.053 475 47 2 993 1467 684646744 684647213 5.900000e-163 584.0
8 TraesCS4D01G346900 chr5A 93.048 374 22 3 2143 2516 12880104 12880473 1.000000e-150 544.0
9 TraesCS4D01G346900 chr5A 91.608 286 20 3 2231 2516 52524242 52524523 3.840000e-105 392.0
10 TraesCS4D01G346900 chr5A 80.783 281 22 11 3844 4092 681895864 681895584 1.500000e-44 191.0
11 TraesCS4D01G346900 chr5A 88.966 145 13 1 2372 2516 296677921 296678062 4.200000e-40 176.0
12 TraesCS4D01G346900 chr5A 90.152 132 10 1 2385 2516 591608041 591608169 7.040000e-38 169.0
13 TraesCS4D01G346900 chr5A 92.593 108 8 0 3844 3951 683634733 683634840 5.480000e-34 156.0
14 TraesCS4D01G346900 chr5A 94.444 72 3 1 3730 3800 681895928 681895857 4.330000e-20 110.0
15 TraesCS4D01G346900 chr5A 94.444 72 3 1 3730 3800 683634669 683634740 4.330000e-20 110.0
16 TraesCS4D01G346900 chr5A 92.537 67 5 0 3844 3910 681895528 681895462 3.370000e-16 97.1
17 TraesCS4D01G346900 chr5A 92.105 38 2 1 3820 3856 7550769 7550732 7.000000e-03 52.8
18 TraesCS4D01G346900 chr4B 94.130 988 44 10 1938 2918 644680909 644679929 0.000000e+00 1491.0
19 TraesCS4D01G346900 chr4B 95.827 695 20 7 764 1456 644682006 644681319 0.000000e+00 1114.0
20 TraesCS4D01G346900 chr4B 89.512 553 16 14 2916 3454 644679816 644679292 0.000000e+00 662.0
21 TraesCS4D01G346900 chr4B 91.266 458 40 0 992 1449 646112703 646113160 3.470000e-175 625.0
22 TraesCS4D01G346900 chr4B 78.468 966 133 43 1695 2634 646113938 646114854 2.760000e-156 562.0
23 TraesCS4D01G346900 chr4B 92.920 339 16 3 1535 1868 644681277 644680942 1.710000e-133 486.0
24 TraesCS4D01G346900 chr4B 90.823 316 18 2 279 590 644682515 644682207 2.940000e-111 412.0
25 TraesCS4D01G346900 chr4B 89.098 266 12 6 3844 4093 644676239 644675975 8.540000e-82 315.0
26 TraesCS4D01G346900 chr4B 91.213 239 8 8 1 230 644682744 644682510 3.070000e-81 313.0
27 TraesCS4D01G346900 chr4B 90.367 218 17 3 3523 3739 644676608 644676394 2.410000e-72 283.0
28 TraesCS4D01G346900 chr4B 97.647 85 1 1 229 312 644707837 644707753 1.190000e-30 145.0
29 TraesCS4D01G346900 chr4B 95.238 84 3 1 3718 3800 644676315 644676232 9.230000e-27 132.0
30 TraesCS4D01G346900 chr4B 95.122 82 4 0 3451 3532 644676738 644676657 3.320000e-26 130.0
31 TraesCS4D01G346900 chr4B 92.982 57 4 0 3851 3907 644675915 644675859 2.620000e-12 84.2
32 TraesCS4D01G346900 chr4B 82.609 69 5 4 3790 3851 70556480 70556548 2.000000e-03 54.7
33 TraesCS4D01G346900 chr2D 79.457 1806 235 85 998 2777 483632976 483631281 0.000000e+00 1155.0
34 TraesCS4D01G346900 chr2D 80.425 848 121 28 998 1835 527491686 527492498 4.530000e-169 604.0
35 TraesCS4D01G346900 chr2D 78.924 688 89 36 1968 2634 527492494 527493146 2.280000e-112 416.0
36 TraesCS4D01G346900 chr2A 79.605 1672 216 84 998 2634 627513549 627511968 0.000000e+00 1083.0
37 TraesCS4D01G346900 chr2A 81.265 854 115 27 992 1835 672368275 672369093 0.000000e+00 649.0
38 TraesCS4D01G346900 chr2A 78.655 684 99 34 1967 2634 672369088 672369740 1.060000e-110 411.0
39 TraesCS4D01G346900 chr2A 96.875 32 0 1 3795 3825 668087565 668087596 7.000000e-03 52.8
40 TraesCS4D01G346900 chr2B 83.547 857 101 24 998 1847 568469093 568468270 0.000000e+00 765.0
41 TraesCS4D01G346900 chr2B 81.499 854 110 31 992 1835 624768154 624768969 0.000000e+00 658.0
42 TraesCS4D01G346900 chr7D 90.050 201 16 2 2376 2575 134508080 134508277 1.460000e-64 257.0
43 TraesCS4D01G346900 chr7D 100.000 28 0 0 3795 3822 124168220 124168193 7.000000e-03 52.8
44 TraesCS4D01G346900 chr3B 86.441 59 5 1 3796 3851 481649527 481649469 1.230000e-05 62.1
45 TraesCS4D01G346900 chr6D 92.683 41 2 1 3815 3854 148535096 148535056 1.590000e-04 58.4
46 TraesCS4D01G346900 chr4A 97.059 34 0 1 3790 3823 703677756 703677788 5.720000e-04 56.5
47 TraesCS4D01G346900 chr4A 100.000 29 0 0 3795 3823 609932642 609932614 2.000000e-03 54.7
48 TraesCS4D01G346900 chr4A 96.970 33 0 1 3790 3822 703626736 703626767 2.000000e-03 54.7
49 TraesCS4D01G346900 chr6B 100.000 29 0 0 3826 3854 566550523 566550551 2.000000e-03 54.7
50 TraesCS4D01G346900 chr3A 90.476 42 3 1 3795 3835 502841284 502841243 2.000000e-03 54.7
51 TraesCS4D01G346900 chr1D 100.000 28 0 0 3795 3822 225544249 225544222 7.000000e-03 52.8
52 TraesCS4D01G346900 chr1D 94.286 35 1 1 3820 3853 493352426 493352392 7.000000e-03 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 TraesCS4D01G346900 chr4D 500715704 500719796 4092 True 7559.000000 7559 100.000000 1 4093 1 chr4D.!!$R1 4092
1 TraesCS4D01G346900 chr4D 502013340 502015153 1813 False 439.666667 603 84.466333 992 2641 3 chr4D.!!$F1 1649
2 TraesCS4D01G346900 chr5A 683630137 683634840 4703 False 1442.333333 4061 92.341667 161 3951 3 chr5A.!!$F5 3790
3 TraesCS4D01G346900 chr5A 681895462 681900389 4927 True 1105.525000 4024 89.383500 161 4092 4 chr5A.!!$R2 3931
4 TraesCS4D01G346900 chr5A 684646744 684648850 2106 False 648.500000 713 84.080500 993 2641 2 chr5A.!!$F6 1648
5 TraesCS4D01G346900 chr4B 646112703 646114854 2151 False 593.500000 625 84.867000 992 2634 2 chr4B.!!$F2 1642
6 TraesCS4D01G346900 chr4B 644675859 644682744 6885 True 492.927273 1491 92.475636 1 4093 11 chr4B.!!$R2 4092
7 TraesCS4D01G346900 chr2D 483631281 483632976 1695 True 1155.000000 1155 79.457000 998 2777 1 chr2D.!!$R1 1779
8 TraesCS4D01G346900 chr2D 527491686 527493146 1460 False 510.000000 604 79.674500 998 2634 2 chr2D.!!$F1 1636
9 TraesCS4D01G346900 chr2A 627511968 627513549 1581 True 1083.000000 1083 79.605000 998 2634 1 chr2A.!!$R1 1636
10 TraesCS4D01G346900 chr2A 672368275 672369740 1465 False 530.000000 649 79.960000 992 2634 2 chr2A.!!$F2 1642
11 TraesCS4D01G346900 chr2B 568468270 568469093 823 True 765.000000 765 83.547000 998 1847 1 chr2B.!!$R1 849
12 TraesCS4D01G346900 chr2B 624768154 624768969 815 False 658.000000 658 81.499000 992 1835 1 chr2B.!!$F1 843

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
197 204 0.179059 TGAAGAGCGCTTTGGTGTGA 60.179 50.0 13.26 0.0 33.61 3.58 F
1616 2575 0.032615 ACAAGGTTGGGGAAGTTGCA 60.033 50.0 0.00 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 3552 0.464554 GCCTCATTCCACCACCTAGC 60.465 60.0 0.0 0.0 0.0 3.42 R
3104 4684 0.110486 ATTCAGGAAGTGTGGCCGTT 59.890 50.0 0.0 0.0 0.0 4.44 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
47 48 2.713531 AAATGTCTGGTGGCCGGCTT 62.714 55.000 28.56 6.12 0.00 4.35
111 112 6.554982 TCTGAGTATTCTGCCACTTGGTATAT 59.445 38.462 0.00 0.00 37.57 0.86
112 113 7.728532 TCTGAGTATTCTGCCACTTGGTATATA 59.271 37.037 0.00 0.00 37.57 0.86
113 114 8.435931 TGAGTATTCTGCCACTTGGTATATAT 57.564 34.615 0.00 0.00 37.57 0.86
114 115 8.531982 TGAGTATTCTGCCACTTGGTATATATC 58.468 37.037 0.00 0.00 37.57 1.63
115 116 8.671987 AGTATTCTGCCACTTGGTATATATCT 57.328 34.615 0.00 0.00 37.57 1.98
117 118 9.726438 GTATTCTGCCACTTGGTATATATCTTT 57.274 33.333 0.00 0.00 37.57 2.52
118 119 8.627208 ATTCTGCCACTTGGTATATATCTTTG 57.373 34.615 0.00 0.00 37.57 2.77
148 155 3.284336 CGTGACCGGTGGAGATGA 58.716 61.111 14.63 0.00 0.00 2.92
152 159 1.066143 GTGACCGGTGGAGATGATTGT 60.066 52.381 14.63 0.00 0.00 2.71
156 163 2.168521 ACCGGTGGAGATGATTGTGTAG 59.831 50.000 6.12 0.00 0.00 2.74
158 165 3.383505 CCGGTGGAGATGATTGTGTAGTA 59.616 47.826 0.00 0.00 0.00 1.82
159 166 4.039245 CCGGTGGAGATGATTGTGTAGTAT 59.961 45.833 0.00 0.00 0.00 2.12
167 174 8.562892 GGAGATGATTGTGTAGTATTGGATTTG 58.437 37.037 0.00 0.00 0.00 2.32
185 192 2.961526 TGTAGACCGGATTGAAGAGC 57.038 50.000 9.46 0.00 0.00 4.09
197 204 0.179059 TGAAGAGCGCTTTGGTGTGA 60.179 50.000 13.26 0.00 33.61 3.58
239 246 7.378966 GTCGGAGATGATTGTATATTTCAGGA 58.621 38.462 0.00 0.00 40.67 3.86
240 247 7.329717 GTCGGAGATGATTGTATATTTCAGGAC 59.670 40.741 0.00 0.00 40.67 3.85
241 248 7.233553 TCGGAGATGATTGTATATTTCAGGACT 59.766 37.037 0.00 0.00 0.00 3.85
242 249 7.543868 CGGAGATGATTGTATATTTCAGGACTC 59.456 40.741 0.00 0.00 0.00 3.36
243 250 8.592809 GGAGATGATTGTATATTTCAGGACTCT 58.407 37.037 0.00 0.00 0.00 3.24
251 258 6.674861 TGTATATTTCAGGACTCTAACCCCAA 59.325 38.462 0.00 0.00 0.00 4.12
293 303 7.087639 GTCTCTGTATATTGTAGCTCCATCAC 58.912 42.308 0.00 0.00 0.00 3.06
570 590 0.248215 CGGATTCTGGTGCGCAAATC 60.248 55.000 14.00 17.69 0.00 2.17
573 593 1.064654 GATTCTGGTGCGCAAATCCTC 59.935 52.381 14.00 0.00 0.00 3.71
606 626 4.982749 GCGGCGGTACCATAGGGC 62.983 72.222 13.54 6.44 39.03 5.19
623 682 1.948145 GGGCTGCTCTTGAATGATGAG 59.052 52.381 0.00 0.00 0.00 2.90
652 711 5.022282 AGATTTGTTGTTTTCCCTTGTGG 57.978 39.130 0.00 0.00 0.00 4.17
656 715 4.625607 TGTTGTTTTCCCTTGTGGTTTT 57.374 36.364 0.00 0.00 34.77 2.43
686 745 3.207669 CATTGGCCGCTCTGCTCC 61.208 66.667 0.00 0.00 0.00 4.70
712 771 1.376543 ATCTCAGCGCAAATGAGTGG 58.623 50.000 20.59 1.70 43.79 4.00
719 778 1.795162 GCGCAAATGAGTGGCATGTAC 60.795 52.381 0.30 0.00 37.28 2.90
776 907 2.434134 GCCATGTCGTCGTCGTGTC 61.434 63.158 10.14 0.00 38.33 3.67
777 908 1.800315 CCATGTCGTCGTCGTGTCC 60.800 63.158 10.14 0.00 38.33 4.02
778 909 2.144069 CATGTCGTCGTCGTGTCCG 61.144 63.158 1.33 0.00 38.33 4.79
780 911 4.380628 GTCGTCGTCGTGTCCGCT 62.381 66.667 1.33 0.00 38.33 5.52
781 912 4.379143 TCGTCGTCGTGTCCGCTG 62.379 66.667 1.33 0.00 38.33 5.18
802 941 0.801067 GTGCTAAGCTGCTGCAATGC 60.801 55.000 18.42 16.76 42.74 3.56
848 990 0.303493 CCGTCCGTATGGCATTTTCG 59.697 55.000 4.78 8.74 34.14 3.46
860 1002 3.935203 TGGCATTTTCGCTTTCTCTAGAG 59.065 43.478 13.98 13.98 0.00 2.43
1164 1306 1.535685 GATCATGGGCAAGGAGGCT 59.464 57.895 0.00 0.00 43.56 4.58
1488 2447 3.868077 GTCTGCTGCTAACTCTGTTATGG 59.132 47.826 0.00 0.00 0.00 2.74
1533 2492 4.620723 AGGTTATGGTACCTGATCTGTCA 58.379 43.478 14.36 0.00 46.71 3.58
1544 2503 6.259550 ACCTGATCTGTCAAGTATTTTTGC 57.740 37.500 0.00 0.00 33.05 3.68
1547 2506 5.702865 TGATCTGTCAAGTATTTTTGCTGC 58.297 37.500 0.00 0.00 0.00 5.25
1556 2515 5.261209 AGTATTTTTGCTGCTGTTGTTGA 57.739 34.783 0.00 0.00 0.00 3.18
1607 2566 4.021102 AGAATACACTGACAAGGTTGGG 57.979 45.455 0.00 0.00 0.00 4.12
1616 2575 0.032615 ACAAGGTTGGGGAAGTTGCA 60.033 50.000 0.00 0.00 0.00 4.08
1796 3049 1.671379 GGCACTTGGAGTTCCCGTC 60.671 63.158 0.00 0.00 37.93 4.79
1865 3232 3.057596 TGCTTGGCACTACACTAAAATGC 60.058 43.478 0.00 0.00 31.71 3.56
2058 3425 7.503566 ACAAAAGGTGATGATGGGTAGATATTG 59.496 37.037 0.00 0.00 0.00 1.90
2121 3516 6.271488 TGCAAGGGAAATCTGACAAATAAG 57.729 37.500 0.00 0.00 0.00 1.73
2154 3552 6.106673 TCAGGCTAAAATTCTTAGGAAGACG 58.893 40.000 0.00 0.00 37.23 4.18
2336 3757 5.181245 CGGCATCGATATAACCCTGAATTTT 59.819 40.000 0.00 0.00 39.00 1.82
2350 3771 6.312672 ACCCTGAATTTTGTTTTCTTTTGTCG 59.687 34.615 0.00 0.00 0.00 4.35
2383 3804 7.771927 AGATGGACTGAAGAAAATCAAACAT 57.228 32.000 0.00 0.00 0.00 2.71
2449 3877 8.688151 AGTCTGTTATTCCATCTAACTACTGAC 58.312 37.037 0.00 0.00 31.15 3.51
2452 3880 8.008513 TGTTATTCCATCTAACTACTGACCTC 57.991 38.462 0.00 0.00 31.71 3.85
2465 3893 4.336889 ACTGACCTCGATGTTTCTTTCA 57.663 40.909 0.00 0.00 0.00 2.69
2466 3894 4.310769 ACTGACCTCGATGTTTCTTTCAG 58.689 43.478 0.00 0.00 36.20 3.02
2468 3896 4.307432 TGACCTCGATGTTTCTTTCAGAC 58.693 43.478 0.00 0.00 0.00 3.51
2470 3912 4.310769 ACCTCGATGTTTCTTTCAGACTG 58.689 43.478 0.00 0.00 0.00 3.51
2643 4086 3.249917 CTTCGCTCAACTTCCTTCTCTC 58.750 50.000 0.00 0.00 0.00 3.20
2645 4088 2.490115 TCGCTCAACTTCCTTCTCTCTC 59.510 50.000 0.00 0.00 0.00 3.20
2646 4089 2.491693 CGCTCAACTTCCTTCTCTCTCT 59.508 50.000 0.00 0.00 0.00 3.10
2647 4090 3.427503 CGCTCAACTTCCTTCTCTCTCTC 60.428 52.174 0.00 0.00 0.00 3.20
2732 4180 2.614057 GTCTGTTTGGACTGGTCAACTG 59.386 50.000 3.10 4.40 33.81 3.16
2741 4189 4.819630 TGGACTGGTCAACTGAAACATTAC 59.180 41.667 3.10 0.00 0.00 1.89
2913 4364 8.122952 CGTTCCAGATTTATATGTTTTGACCTC 58.877 37.037 0.00 0.00 0.00 3.85
2996 4573 3.138839 TGCTGTGATTGGTGGGATATCAT 59.861 43.478 4.83 0.00 31.58 2.45
2997 4574 4.350520 TGCTGTGATTGGTGGGATATCATA 59.649 41.667 4.83 0.00 31.58 2.15
2998 4575 5.014438 TGCTGTGATTGGTGGGATATCATAT 59.986 40.000 4.83 0.00 31.58 1.78
2999 4576 5.587844 GCTGTGATTGGTGGGATATCATATC 59.412 44.000 4.83 0.00 31.58 1.63
3000 4577 6.700845 TGTGATTGGTGGGATATCATATCA 57.299 37.500 6.99 0.00 31.58 2.15
3086 4666 1.153329 TTGTTCGACCAACGGCACT 60.153 52.632 0.00 0.00 42.82 4.40
3094 4674 1.878522 CCAACGGCACTAGCTAGCG 60.879 63.158 20.91 17.59 41.70 4.26
3095 4675 2.202756 AACGGCACTAGCTAGCGC 60.203 61.111 22.81 22.81 41.70 5.92
3096 4676 4.554363 ACGGCACTAGCTAGCGCG 62.554 66.667 23.64 20.45 42.32 6.86
3098 4678 3.900892 GGCACTAGCTAGCGCGGA 61.901 66.667 23.64 0.00 42.32 5.54
3099 4679 2.336809 GCACTAGCTAGCGCGGAT 59.663 61.111 20.91 0.00 42.32 4.18
3100 4680 1.300233 GCACTAGCTAGCGCGGATT 60.300 57.895 20.91 0.00 42.32 3.01
3101 4681 1.278849 GCACTAGCTAGCGCGGATTC 61.279 60.000 20.91 0.00 42.32 2.52
3102 4682 0.030773 CACTAGCTAGCGCGGATTCA 59.969 55.000 20.91 0.00 42.32 2.57
3103 4683 0.962489 ACTAGCTAGCGCGGATTCAT 59.038 50.000 20.91 0.00 42.32 2.57
3104 4684 2.095212 CACTAGCTAGCGCGGATTCATA 60.095 50.000 20.91 0.00 42.32 2.15
3105 4685 2.557056 ACTAGCTAGCGCGGATTCATAA 59.443 45.455 20.91 0.00 42.32 1.90
3106 4686 1.784525 AGCTAGCGCGGATTCATAAC 58.215 50.000 8.83 0.00 42.32 1.89
3118 4698 1.816074 TTCATAACGGCCACACTTCC 58.184 50.000 2.24 0.00 0.00 3.46
3191 4774 1.106351 TGGATTGCCTGTTTGTGCGT 61.106 50.000 0.00 0.00 34.31 5.24
3350 4933 1.895131 GTTTGACCGTAGTACCCCTCA 59.105 52.381 0.00 0.00 0.00 3.86
3554 8459 4.750833 TTTTTGATTAGTGGGAAGGGGA 57.249 40.909 0.00 0.00 0.00 4.81
3556 8461 1.213296 TGATTAGTGGGAAGGGGAGC 58.787 55.000 0.00 0.00 0.00 4.70
3557 8462 0.474614 GATTAGTGGGAAGGGGAGCC 59.525 60.000 0.00 0.00 0.00 4.70
3571 8476 1.032114 GGAGCCCACCCTGAAATTCG 61.032 60.000 0.00 0.00 0.00 3.34
3600 8505 7.650104 GGGAGAGATTAATTAGAGAAAGACACG 59.350 40.741 0.00 0.00 0.00 4.49
3602 8507 9.228636 GAGAGATTAATTAGAGAAAGACACGTC 57.771 37.037 0.00 0.00 0.00 4.34
3621 8526 9.740239 GACACGTCTTCATGTAAGGTAATTATA 57.260 33.333 0.00 0.00 35.75 0.98
3645 8550 2.685100 ACTTGCTTTCGTAGGTGTAGC 58.315 47.619 0.00 0.00 0.00 3.58
3680 8585 2.695127 AAGCTCTCTCAAGATGGCTG 57.305 50.000 7.36 0.00 34.04 4.85
3691 8596 1.269958 AGATGGCTGACACTAGCACA 58.730 50.000 0.00 0.00 45.46 4.57
3788 8936 2.745821 CGCCCCTAAGTAAAACCTTGTC 59.254 50.000 0.00 0.00 0.00 3.18
3789 8937 2.745821 GCCCCTAAGTAAAACCTTGTCG 59.254 50.000 0.00 0.00 0.00 4.35
3790 8938 3.808265 GCCCCTAAGTAAAACCTTGTCGT 60.808 47.826 0.00 0.00 0.00 4.34
3791 8939 4.563374 GCCCCTAAGTAAAACCTTGTCGTA 60.563 45.833 0.00 0.00 0.00 3.43
3793 8941 6.175471 CCCCTAAGTAAAACCTTGTCGTAAT 58.825 40.000 0.00 0.00 0.00 1.89
3794 8942 6.093082 CCCCTAAGTAAAACCTTGTCGTAATG 59.907 42.308 0.00 0.00 0.00 1.90
3795 8943 6.652062 CCCTAAGTAAAACCTTGTCGTAATGT 59.348 38.462 0.00 0.00 0.00 2.71
3796 8944 7.818930 CCCTAAGTAAAACCTTGTCGTAATGTA 59.181 37.037 0.00 0.00 0.00 2.29
3797 8945 8.866956 CCTAAGTAAAACCTTGTCGTAATGTAG 58.133 37.037 0.00 0.00 0.00 2.74
3798 8946 9.415544 CTAAGTAAAACCTTGTCGTAATGTAGT 57.584 33.333 0.00 0.00 0.00 2.73
3800 8948 8.748380 AGTAAAACCTTGTCGTAATGTAGTAC 57.252 34.615 0.00 0.00 0.00 2.73
3801 8949 8.579863 AGTAAAACCTTGTCGTAATGTAGTACT 58.420 33.333 0.00 0.00 0.00 2.73
3802 8950 9.196552 GTAAAACCTTGTCGTAATGTAGTACTT 57.803 33.333 0.00 0.00 0.00 2.24
3803 8951 7.880059 AAACCTTGTCGTAATGTAGTACTTC 57.120 36.000 0.00 0.00 0.00 3.01
3804 8952 5.958955 ACCTTGTCGTAATGTAGTACTTCC 58.041 41.667 0.00 0.00 0.00 3.46
3805 8953 5.713861 ACCTTGTCGTAATGTAGTACTTCCT 59.286 40.000 0.00 0.00 0.00 3.36
3806 8954 6.127786 ACCTTGTCGTAATGTAGTACTTCCTC 60.128 42.308 0.00 0.00 0.00 3.71
3807 8955 5.824904 TGTCGTAATGTAGTACTTCCTCC 57.175 43.478 0.00 0.00 0.00 4.30
3808 8956 4.333649 TGTCGTAATGTAGTACTTCCTCCG 59.666 45.833 0.00 0.00 0.00 4.63
3809 8957 4.333926 GTCGTAATGTAGTACTTCCTCCGT 59.666 45.833 0.00 0.00 0.00 4.69
3810 8958 5.523916 GTCGTAATGTAGTACTTCCTCCGTA 59.476 44.000 0.00 0.00 0.00 4.02
3811 8959 6.037172 GTCGTAATGTAGTACTTCCTCCGTAA 59.963 42.308 0.00 0.00 0.00 3.18
3812 8960 6.597672 TCGTAATGTAGTACTTCCTCCGTAAA 59.402 38.462 0.00 0.00 0.00 2.01
3813 8961 6.688813 CGTAATGTAGTACTTCCTCCGTAAAC 59.311 42.308 0.00 0.00 0.00 2.01
3814 8962 6.847421 AATGTAGTACTTCCTCCGTAAACT 57.153 37.500 0.00 0.00 0.00 2.66
3815 8963 7.944729 AATGTAGTACTTCCTCCGTAAACTA 57.055 36.000 0.00 0.00 0.00 2.24
3816 8964 7.944729 ATGTAGTACTTCCTCCGTAAACTAA 57.055 36.000 0.00 0.00 0.00 2.24
3817 8965 7.944729 TGTAGTACTTCCTCCGTAAACTAAT 57.055 36.000 0.00 0.00 0.00 1.73
3818 8966 9.632638 ATGTAGTACTTCCTCCGTAAACTAATA 57.367 33.333 0.00 0.00 0.00 0.98
3819 8967 9.632638 TGTAGTACTTCCTCCGTAAACTAATAT 57.367 33.333 0.00 0.00 0.00 1.28
3934 9082 7.027874 ACCCCTGTCTCAAAATATAAGAACA 57.972 36.000 0.00 0.00 0.00 3.18
4028 9206 4.852609 AAAACGTCCTATATGTTGCGAC 57.147 40.909 0.00 0.00 37.39 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.541588 GGCCACCAGACATTTCTCAAC 59.458 52.381 0.00 0.00 0.00 3.18
23 24 1.881925 CGGCCACCAGACATTTCTCAA 60.882 52.381 2.24 0.00 0.00 3.02
47 48 2.273179 CCTCACTCGTGGGTTCCGA 61.273 63.158 0.00 0.00 0.00 4.55
111 112 3.070446 ACGGTCAGTTCACACCAAAGATA 59.930 43.478 0.00 0.00 32.33 1.98
112 113 2.158813 ACGGTCAGTTCACACCAAAGAT 60.159 45.455 0.00 0.00 32.33 2.40
113 114 1.208535 ACGGTCAGTTCACACCAAAGA 59.791 47.619 0.00 0.00 32.33 2.52
114 115 1.330521 CACGGTCAGTTCACACCAAAG 59.669 52.381 0.00 0.00 32.33 2.77
115 116 1.066071 TCACGGTCAGTTCACACCAAA 60.066 47.619 0.00 0.00 32.33 3.28
117 118 0.179094 GTCACGGTCAGTTCACACCA 60.179 55.000 0.00 0.00 32.33 4.17
118 119 0.878961 GGTCACGGTCAGTTCACACC 60.879 60.000 0.00 0.00 0.00 4.16
148 155 7.494625 CGGTCTACAAATCCAATACTACACAAT 59.505 37.037 0.00 0.00 0.00 2.71
152 159 5.657745 TCCGGTCTACAAATCCAATACTACA 59.342 40.000 0.00 0.00 0.00 2.74
156 163 6.053005 TCAATCCGGTCTACAAATCCAATAC 58.947 40.000 0.00 0.00 0.00 1.89
158 165 5.110814 TCAATCCGGTCTACAAATCCAAT 57.889 39.130 0.00 0.00 0.00 3.16
159 166 4.561500 TCAATCCGGTCTACAAATCCAA 57.438 40.909 0.00 0.00 0.00 3.53
167 174 1.841450 CGCTCTTCAATCCGGTCTAC 58.159 55.000 0.00 0.00 0.00 2.59
185 192 1.597937 GCTCACTTTCACACCAAAGCG 60.598 52.381 0.00 0.00 36.93 4.68
197 204 0.318784 GACGTCGGTCTGCTCACTTT 60.319 55.000 0.00 0.00 40.15 2.66
231 238 3.267031 CCTTGGGGTTAGAGTCCTGAAAT 59.733 47.826 0.00 0.00 0.00 2.17
233 240 2.266279 CCTTGGGGTTAGAGTCCTGAA 58.734 52.381 0.00 0.00 0.00 3.02
235 242 0.912486 CCCTTGGGGTTAGAGTCCTG 59.088 60.000 0.00 0.00 38.25 3.86
236 243 0.797579 TCCCTTGGGGTTAGAGTCCT 59.202 55.000 5.78 0.00 44.74 3.85
237 244 1.205055 CTCCCTTGGGGTTAGAGTCC 58.795 60.000 5.78 0.00 44.74 3.85
239 246 0.253207 CCCTCCCTTGGGGTTAGAGT 60.253 60.000 5.78 0.00 44.74 3.24
240 247 2.621486 CCCTCCCTTGGGGTTAGAG 58.379 63.158 5.78 0.00 44.74 2.43
241 248 4.933607 CCCTCCCTTGGGGTTAGA 57.066 61.111 5.78 0.00 44.74 2.10
251 258 1.073706 ACCAAGTGACACCCTCCCT 60.074 57.895 0.84 0.00 0.00 4.20
254 261 1.001406 CAGAGACCAAGTGACACCCTC 59.999 57.143 0.84 2.25 0.00 4.30
258 265 6.398918 ACAATATACAGAGACCAAGTGACAC 58.601 40.000 0.00 0.00 0.00 3.67
261 268 6.607600 AGCTACAATATACAGAGACCAAGTGA 59.392 38.462 0.00 0.00 0.00 3.41
262 269 6.810911 AGCTACAATATACAGAGACCAAGTG 58.189 40.000 0.00 0.00 0.00 3.16
293 303 1.305930 GGTGGCCCGTTGCTTTCTAG 61.306 60.000 0.00 0.00 40.92 2.43
539 559 0.674534 AGAATCCGGATGTAGCGGAC 59.325 55.000 19.95 2.75 34.41 4.79
540 560 0.673985 CAGAATCCGGATGTAGCGGA 59.326 55.000 19.95 0.00 36.17 5.54
570 590 2.289565 GCTGGAACGGATAAAAGGAGG 58.710 52.381 0.00 0.00 36.31 4.30
595 615 1.762957 TCAAGAGCAGCCCTATGGTAC 59.237 52.381 0.00 0.00 0.00 3.34
606 626 1.598132 CGCCTCATCATTCAAGAGCAG 59.402 52.381 0.00 0.00 0.00 4.24
623 682 3.571571 GAAAACAACAAATCTACCCGCC 58.428 45.455 0.00 0.00 0.00 6.13
652 711 3.495753 CCAATGCAAGGCTCTTGAAAAAC 59.504 43.478 16.28 2.25 0.00 2.43
676 735 2.351111 GAGATTTTTCAGGAGCAGAGCG 59.649 50.000 0.00 0.00 0.00 5.03
686 745 4.478699 TCATTTGCGCTGAGATTTTTCAG 58.521 39.130 9.73 0.00 45.85 3.02
712 771 1.241315 ACTTTGGTGCCCGTACATGC 61.241 55.000 0.00 0.00 0.00 4.06
719 778 2.260869 CCACAGACTTTGGTGCCCG 61.261 63.158 0.00 0.00 33.72 6.13
778 909 3.123620 AGCAGCTTAGCACGCAGC 61.124 61.111 18.29 8.89 46.19 5.25
780 911 3.425713 GCAGCAGCTTAGCACGCA 61.426 61.111 18.29 0.00 37.91 5.24
781 912 2.262471 ATTGCAGCAGCTTAGCACGC 62.262 55.000 7.07 8.82 42.74 5.34
782 913 0.522705 CATTGCAGCAGCTTAGCACG 60.523 55.000 7.07 0.00 42.74 5.34
784 915 1.245376 TGCATTGCAGCAGCTTAGCA 61.245 50.000 7.38 3.29 40.11 3.49
802 941 6.690957 TCTGCTTTTGATTCGTTTTTGTACTG 59.309 34.615 0.00 0.00 0.00 2.74
1164 1306 3.319198 GAGGGGACGAACAGGGCA 61.319 66.667 0.00 0.00 0.00 5.36
1512 2471 5.104900 ACTTGACAGATCAGGTACCATAACC 60.105 44.000 15.94 0.00 42.97 2.85
1513 2472 5.978814 ACTTGACAGATCAGGTACCATAAC 58.021 41.667 15.94 2.89 42.97 1.89
1514 2473 7.914427 ATACTTGACAGATCAGGTACCATAA 57.086 36.000 15.94 0.00 46.65 1.90
1515 2474 7.914427 AATACTTGACAGATCAGGTACCATA 57.086 36.000 15.94 0.99 46.65 2.74
1516 2475 6.814954 AATACTTGACAGATCAGGTACCAT 57.185 37.500 15.94 0.00 46.65 3.55
1517 2476 6.620877 AAATACTTGACAGATCAGGTACCA 57.379 37.500 15.94 0.00 46.65 3.25
1518 2477 7.626452 GCAAAAATACTTGACAGATCAGGTACC 60.626 40.741 2.73 2.73 46.65 3.34
1519 2478 7.119846 AGCAAAAATACTTGACAGATCAGGTAC 59.880 37.037 1.85 0.00 46.65 3.34
1521 2480 6.006449 AGCAAAAATACTTGACAGATCAGGT 58.994 36.000 0.00 0.00 46.23 4.00
1522 2481 6.320171 CAGCAAAAATACTTGACAGATCAGG 58.680 40.000 0.00 0.00 37.92 3.86
1523 2482 5.798934 GCAGCAAAAATACTTGACAGATCAG 59.201 40.000 0.00 0.00 35.83 2.90
1524 2483 5.474532 AGCAGCAAAAATACTTGACAGATCA 59.525 36.000 0.00 0.00 0.00 2.92
1525 2484 5.798934 CAGCAGCAAAAATACTTGACAGATC 59.201 40.000 0.00 0.00 0.00 2.75
1526 2485 5.242393 ACAGCAGCAAAAATACTTGACAGAT 59.758 36.000 0.00 0.00 0.00 2.90
1527 2486 4.580167 ACAGCAGCAAAAATACTTGACAGA 59.420 37.500 0.00 0.00 0.00 3.41
1528 2487 4.863491 ACAGCAGCAAAAATACTTGACAG 58.137 39.130 0.00 0.00 0.00 3.51
1529 2488 4.916983 ACAGCAGCAAAAATACTTGACA 57.083 36.364 0.00 0.00 0.00 3.58
1530 2489 5.043248 ACAACAGCAGCAAAAATACTTGAC 58.957 37.500 0.00 0.00 0.00 3.18
1531 2490 5.261209 ACAACAGCAGCAAAAATACTTGA 57.739 34.783 0.00 0.00 0.00 3.02
1532 2491 5.519566 TCAACAACAGCAGCAAAAATACTTG 59.480 36.000 0.00 0.00 0.00 3.16
1533 2492 5.659463 TCAACAACAGCAGCAAAAATACTT 58.341 33.333 0.00 0.00 0.00 2.24
1547 2506 2.620115 ACCAGAACTGCATCAACAACAG 59.380 45.455 0.00 0.00 37.45 3.16
1556 2515 0.773644 ACTTCCCACCAGAACTGCAT 59.226 50.000 0.00 0.00 0.00 3.96
1607 2566 1.067354 CCATGAGCCTTTGCAACTTCC 60.067 52.381 0.00 0.00 41.13 3.46
1817 3070 7.657761 AGATTGATACATACCGAAACTGAATCC 59.342 37.037 0.00 0.00 0.00 3.01
1888 3255 5.517924 TCAGCCCATTTTCCATTCTTATGA 58.482 37.500 0.00 0.00 33.37 2.15
2058 3425 5.563842 CAGCTTAAACTTACTAGCATGCAC 58.436 41.667 21.98 0.00 36.11 4.57
2154 3552 0.464554 GCCTCATTCCACCACCTAGC 60.465 60.000 0.00 0.00 0.00 3.42
2336 3757 7.309177 TCTGAACATTTCGACAAAAGAAAACA 58.691 30.769 0.00 0.00 40.44 2.83
2383 3804 6.404623 CCACTGAAGTCAAATCAACTGTGAAA 60.405 38.462 0.00 0.00 37.30 2.69
2441 3866 5.010719 TGAAAGAAACATCGAGGTCAGTAGT 59.989 40.000 1.92 0.00 0.00 2.73
2465 3893 5.882557 GGGTCACAAACATGATATTCAGTCT 59.117 40.000 0.00 0.00 0.00 3.24
2466 3894 5.066505 GGGGTCACAAACATGATATTCAGTC 59.933 44.000 0.00 0.00 0.00 3.51
2468 3896 4.339247 GGGGGTCACAAACATGATATTCAG 59.661 45.833 0.00 0.00 0.00 3.02
2470 3912 3.315191 CGGGGGTCACAAACATGATATTC 59.685 47.826 0.00 0.00 0.00 1.75
2677 4121 7.126061 TGATTCTTATAGTGAGGAGTTGAGGA 58.874 38.462 0.00 0.00 0.00 3.71
2732 4180 9.601971 TTTTGACTAAATACAGCGTAATGTTTC 57.398 29.630 0.00 0.00 34.56 2.78
2741 4189 5.280678 GCGTTTCTTTTGACTAAATACAGCG 59.719 40.000 0.00 0.00 0.00 5.18
2913 4364 2.654749 TCAGAGCAACGGTGATACAG 57.345 50.000 3.55 0.00 0.00 2.74
2996 4573 4.541973 ACAGAGCAACATGTCAGTGATA 57.458 40.909 0.00 0.00 0.00 2.15
2997 4574 3.413846 ACAGAGCAACATGTCAGTGAT 57.586 42.857 0.00 0.00 0.00 3.06
2998 4575 2.916702 ACAGAGCAACATGTCAGTGA 57.083 45.000 0.00 0.00 0.00 3.41
2999 4576 3.304257 GGAAACAGAGCAACATGTCAGTG 60.304 47.826 0.00 0.00 0.00 3.66
3000 4577 2.880890 GGAAACAGAGCAACATGTCAGT 59.119 45.455 0.00 0.00 0.00 3.41
3086 4666 2.667448 CGTTATGAATCCGCGCTAGCTA 60.667 50.000 13.93 0.00 42.32 3.32
3094 4674 1.092921 TGTGGCCGTTATGAATCCGC 61.093 55.000 0.00 0.00 0.00 5.54
3095 4675 0.655733 GTGTGGCCGTTATGAATCCG 59.344 55.000 0.00 0.00 0.00 4.18
3096 4676 2.038387 AGTGTGGCCGTTATGAATCC 57.962 50.000 0.00 0.00 0.00 3.01
3097 4677 2.354821 GGAAGTGTGGCCGTTATGAATC 59.645 50.000 0.00 0.00 0.00 2.52
3098 4678 2.026262 AGGAAGTGTGGCCGTTATGAAT 60.026 45.455 0.00 0.00 0.00 2.57
3099 4679 1.349688 AGGAAGTGTGGCCGTTATGAA 59.650 47.619 0.00 0.00 0.00 2.57
3100 4680 0.981183 AGGAAGTGTGGCCGTTATGA 59.019 50.000 0.00 0.00 0.00 2.15
3101 4681 1.086696 CAGGAAGTGTGGCCGTTATG 58.913 55.000 0.00 0.00 0.00 1.90
3102 4682 0.981183 TCAGGAAGTGTGGCCGTTAT 59.019 50.000 0.00 0.00 0.00 1.89
3103 4683 0.759959 TTCAGGAAGTGTGGCCGTTA 59.240 50.000 0.00 0.00 0.00 3.18
3104 4684 0.110486 ATTCAGGAAGTGTGGCCGTT 59.890 50.000 0.00 0.00 0.00 4.44
3105 4685 0.110486 AATTCAGGAAGTGTGGCCGT 59.890 50.000 0.00 0.00 0.00 5.68
3106 4686 1.737793 GTAATTCAGGAAGTGTGGCCG 59.262 52.381 0.00 0.00 0.00 6.13
3118 4698 7.645402 TCATGCATAGCAATCAAGTAATTCAG 58.355 34.615 0.00 0.00 43.62 3.02
3350 4933 2.028658 CAGGTGGATCGATCATTCGGAT 60.029 50.000 25.93 3.14 45.53 4.18
3422 5711 2.084546 CTCGTTCCCCAAAAGATCACC 58.915 52.381 0.00 0.00 0.00 4.02
3423 5712 1.468914 GCTCGTTCCCCAAAAGATCAC 59.531 52.381 0.00 0.00 0.00 3.06
3425 5714 0.727398 CGCTCGTTCCCCAAAAGATC 59.273 55.000 0.00 0.00 0.00 2.75
3431 5720 2.345991 CCTTCGCTCGTTCCCCAA 59.654 61.111 0.00 0.00 0.00 4.12
3476 8322 2.477176 GCAGTGACCAAACGCCACA 61.477 57.895 0.00 0.00 33.53 4.17
3554 8459 1.000896 CCGAATTTCAGGGTGGGCT 60.001 57.895 0.00 0.00 0.00 5.19
3556 8461 1.379843 CCCCGAATTTCAGGGTGGG 60.380 63.158 18.68 10.81 46.17 4.61
3557 8462 1.379843 CCCCCGAATTTCAGGGTGG 60.380 63.158 15.19 14.29 46.17 4.61
3636 8541 1.760613 CTCCCGGAAATGCTACACCTA 59.239 52.381 0.73 0.00 0.00 3.08
3645 8550 0.108662 GCTTTTGCCTCCCGGAAATG 60.109 55.000 0.73 0.00 40.15 2.32
3788 8936 4.889832 ACGGAGGAAGTACTACATTACG 57.110 45.455 0.00 0.00 0.00 3.18
3789 8937 7.766283 AGTTTACGGAGGAAGTACTACATTAC 58.234 38.462 0.00 0.00 0.00 1.89
3790 8938 7.944729 AGTTTACGGAGGAAGTACTACATTA 57.055 36.000 0.00 0.00 0.00 1.90
3791 8939 6.847421 AGTTTACGGAGGAAGTACTACATT 57.153 37.500 0.00 0.00 0.00 2.71
3793 8941 7.944729 ATTAGTTTACGGAGGAAGTACTACA 57.055 36.000 0.00 0.00 0.00 2.74
3839 8987 9.787435 TTTTGTAAACAGTATTACTCCATCTGT 57.213 29.630 0.00 0.00 40.40 3.41
3841 8989 9.787435 TGTTTTGTAAACAGTATTACTCCATCT 57.213 29.630 1.10 0.00 36.84 2.90
4015 9193 3.243434 ACTTCCTCCGTCGCAACATATAG 60.243 47.826 0.00 0.00 0.00 1.31
4028 9206 9.813446 AACTAATGTAGTAAAATACTTCCTCCG 57.187 33.333 0.00 0.00 38.26 4.63


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

AutoCloner maintained by Alex Coulton.