Multiple sequence alignment - TraesCS4D01G064300

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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 TraesCS4D01G064300 chr4D 100.000 3908 0 0 1 3908 39613590 39609683 0.000000e+00 7217.0
1 TraesCS4D01G064300 chr4D 86.442 1630 172 28 1058 2660 39600617 39602224 0.000000e+00 1740.0
2 TraesCS4D01G064300 chr4D 87.108 830 98 2 1495 2318 39846748 39845922 0.000000e+00 931.0
3 TraesCS4D01G064300 chr4D 89.216 204 22 0 2333 2536 39621413 39621210 5.010000e-64 255.0
4 TraesCS4D01G064300 chr4B 93.216 1754 92 6 937 2686 58064190 58062460 0.000000e+00 2555.0
5 TraesCS4D01G064300 chr4B 86.505 1571 167 27 1058 2603 58031187 58032737 0.000000e+00 1685.0
6 TraesCS4D01G064300 chr4B 89.744 936 93 3 1 935 58065166 58064233 0.000000e+00 1194.0
7 TraesCS4D01G064300 chr4B 83.949 623 88 4 1648 2264 58069132 58068516 1.560000e-163 586.0
8 TraesCS4D01G064300 chr4B 96.729 214 7 0 3695 3908 58062391 58062178 1.340000e-94 357.0
9 TraesCS4D01G064300 chr4B 85.560 277 37 3 2260 2536 58068032 58067759 1.780000e-73 287.0
10 TraesCS4D01G064300 chr4A 86.228 1612 173 30 1058 2643 560745176 560743588 0.000000e+00 1701.0
11 TraesCS4D01G064300 chr4A 88.448 554 43 13 3141 3687 56720966 56721505 0.000000e+00 649.0
12 TraesCS4D01G064300 chr7D 89.181 684 61 6 3016 3689 140319463 140320143 0.000000e+00 841.0
13 TraesCS4D01G064300 chr7D 87.293 181 18 4 34 213 183718924 183718748 6.620000e-48 202.0
14 TraesCS4D01G064300 chr1A 86.582 708 70 11 2996 3693 278645006 278644314 0.000000e+00 758.0
15 TraesCS4D01G064300 chr1A 85.000 220 23 2 2686 2905 278645512 278645303 8.500000e-52 215.0
16 TraesCS4D01G064300 chr6D 86.892 679 59 14 3023 3691 108774652 108773994 0.000000e+00 734.0
17 TraesCS4D01G064300 chr6D 90.268 298 29 0 2705 3002 108775388 108775091 1.320000e-104 390.0
18 TraesCS4D01G064300 chr1D 89.693 553 46 5 3016 3561 213343393 213343941 0.000000e+00 695.0
19 TraesCS4D01G064300 chr1D 86.025 322 27 10 2685 3000 213342457 213342766 2.910000e-86 329.0
20 TraesCS4D01G064300 chr2A 87.189 523 49 9 2996 3507 169345146 169344631 2.620000e-161 579.0
21 TraesCS4D01G064300 chr7B 76.327 490 108 8 231 719 234075562 234075080 5.010000e-64 255.0
22 TraesCS4D01G064300 chr3A 86.854 213 21 6 2 213 549225867 549226073 8.440000e-57 231.0
23 TraesCS4D01G064300 chr2D 86.829 205 19 4 1 204 521506453 521506650 5.080000e-54 222.0
24 TraesCS4D01G064300 chr2D 84.038 213 27 5 2 213 19630296 19630502 8.560000e-47 198.0
25 TraesCS4D01G064300 chr5A 83.333 234 32 6 2 232 673442570 673442341 3.960000e-50 209.0
26 TraesCS4D01G064300 chr3D 84.112 214 20 7 1 213 408313521 408313321 1.110000e-45 195.0
27 TraesCS4D01G064300 chr5D 87.059 170 16 1 52 221 458721503 458721340 1.850000e-43 187.0
28 TraesCS4D01G064300 chr5D 81.860 215 30 6 2 213 458732750 458732542 5.190000e-39 172.0
29 TraesCS4D01G064300 chr1B 83.065 124 21 0 3566 3689 644277335 644277212 3.190000e-21 113.0
30 TraesCS4D01G064300 chr1B 86.792 53 7 0 2687 2739 644279462 644279410 4.220000e-05 60.2


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 TraesCS4D01G064300 chr4D 39609683 39613590 3907 True 7217.0 7217 100.0000 1 3908 1 chr4D.!!$R1 3907
1 TraesCS4D01G064300 chr4D 39600617 39602224 1607 False 1740.0 1740 86.4420 1058 2660 1 chr4D.!!$F1 1602
2 TraesCS4D01G064300 chr4D 39845922 39846748 826 True 931.0 931 87.1080 1495 2318 1 chr4D.!!$R3 823
3 TraesCS4D01G064300 chr4B 58031187 58032737 1550 False 1685.0 1685 86.5050 1058 2603 1 chr4B.!!$F1 1545
4 TraesCS4D01G064300 chr4B 58062178 58069132 6954 True 995.8 2555 89.8396 1 3908 5 chr4B.!!$R1 3907
5 TraesCS4D01G064300 chr4A 560743588 560745176 1588 True 1701.0 1701 86.2280 1058 2643 1 chr4A.!!$R1 1585
6 TraesCS4D01G064300 chr4A 56720966 56721505 539 False 649.0 649 88.4480 3141 3687 1 chr4A.!!$F1 546
7 TraesCS4D01G064300 chr7D 140319463 140320143 680 False 841.0 841 89.1810 3016 3689 1 chr7D.!!$F1 673
8 TraesCS4D01G064300 chr1A 278644314 278645512 1198 True 486.5 758 85.7910 2686 3693 2 chr1A.!!$R1 1007
9 TraesCS4D01G064300 chr6D 108773994 108775388 1394 True 562.0 734 88.5800 2705 3691 2 chr6D.!!$R1 986
10 TraesCS4D01G064300 chr1D 213342457 213343941 1484 False 512.0 695 87.8590 2685 3561 2 chr1D.!!$F1 876
11 TraesCS4D01G064300 chr2A 169344631 169345146 515 True 579.0 579 87.1890 2996 3507 1 chr2A.!!$R1 511

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
785 4752 0.173481 GCAAGGAAAAAGGATCCGGC 59.827 55.0 5.98 0.0 42.03 6.13 F
901 4868 0.240945 AGCTGAAAAATTCGCCCACG 59.759 50.0 0.00 0.0 42.01 4.94 F
2203 6248 0.249657 GCTACCATCCAGGAAGCTCG 60.250 60.0 3.84 0.0 41.22 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 6700 0.615331 TGCAGAGGGATCCACTCAAC 59.385 55.0 23.98 17.71 37.43 3.18 R
2847 6910 0.813821 GACCCACACGTAGGTAGGAC 59.186 60.0 4.23 0.00 36.17 3.85 R
3493 8602 0.249398 CACTAGCCACTACACCACCC 59.751 60.0 0.00 0.00 0.00 4.61 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
20 3987 0.872388 GTTTGCGGGATCTGTTTCGT 59.128 50.000 0.00 0.00 0.00 3.85
23 3990 1.741770 GCGGGATCTGTTTCGTGCT 60.742 57.895 0.00 0.00 0.00 4.40
24 3991 1.970917 GCGGGATCTGTTTCGTGCTG 61.971 60.000 0.00 0.00 0.00 4.41
27 3994 1.610624 GGGATCTGTTTCGTGCTGGAA 60.611 52.381 0.00 0.00 0.00 3.53
28 3995 1.734465 GGATCTGTTTCGTGCTGGAAG 59.266 52.381 0.00 0.00 0.00 3.46
95 4062 9.518906 CAAGTGCTTGCATATGAATATACAAAA 57.481 29.630 6.97 0.00 33.45 2.44
134 4101 9.579932 TCTACATCACTAGTTCATCATCATACT 57.420 33.333 0.00 0.00 0.00 2.12
158 4125 6.845758 AGTTCATCACATCCAAAATCATGT 57.154 33.333 0.00 0.00 33.29 3.21
175 4142 2.004583 TGTGCAACATACGAGGTAGC 57.995 50.000 0.00 0.00 45.67 3.58
178 4145 2.348666 GTGCAACATACGAGGTAGCAAG 59.651 50.000 0.00 0.00 36.32 4.01
264 4231 3.400439 TTTTTACCTGCCGGACGTT 57.600 47.368 5.05 0.00 0.00 3.99
280 4247 2.400399 ACGTTTCATCGAACACGTGAT 58.600 42.857 25.01 11.26 37.62 3.06
283 4250 3.849708 CGTTTCATCGAACACGTGATAGA 59.150 43.478 25.01 17.13 0.00 1.98
347 4314 1.613630 GAGGTGGAGAAGGAGCCCA 60.614 63.158 0.00 0.00 0.00 5.36
398 4365 4.988598 CTTCGCCCGTGCACCAGT 62.989 66.667 12.15 0.00 37.32 4.00
429 4396 1.625818 GAGGCAGTCTTCTTTCTCCCA 59.374 52.381 0.00 0.00 0.00 4.37
434 4401 0.685660 GTCTTCTTTCTCCCACCGGT 59.314 55.000 0.00 0.00 0.00 5.28
532 4499 2.665000 CCTGCCGCTTCCTCTTGA 59.335 61.111 0.00 0.00 0.00 3.02
536 4503 2.815647 CCGCTTCCTCTTGACGCC 60.816 66.667 0.00 0.00 34.89 5.68
537 4504 3.181967 CGCTTCCTCTTGACGCCG 61.182 66.667 0.00 0.00 34.89 6.46
552 4519 4.763646 CCGGCGGCGGAAGGTTTA 62.764 66.667 44.11 0.00 0.00 2.01
553 4520 3.192922 CGGCGGCGGAAGGTTTAG 61.193 66.667 25.36 0.00 0.00 1.85
621 4588 2.480555 GACATTGGAGGTTGCGCG 59.519 61.111 0.00 0.00 0.00 6.86
622 4589 2.031919 ACATTGGAGGTTGCGCGA 59.968 55.556 12.10 0.00 0.00 5.87
641 4608 3.672293 CGCATGATATGGGCCACC 58.328 61.111 9.28 1.19 36.40 4.61
662 4629 3.261897 CCTGGAGGTTGTGAGTACTTCAT 59.738 47.826 0.00 0.00 38.29 2.57
668 4635 4.348168 AGGTTGTGAGTACTTCATCTGGTT 59.652 41.667 0.00 0.00 38.29 3.67
677 4644 2.884639 ACTTCATCTGGTTTGTTTCCGG 59.115 45.455 0.00 0.00 0.00 5.14
679 4646 0.958091 CATCTGGTTTGTTTCCGGCA 59.042 50.000 0.00 0.00 0.00 5.69
695 4662 4.457496 CACTGCGAGGCCGGACAT 62.457 66.667 11.69 0.00 36.06 3.06
702 4669 2.683933 AGGCCGGACATCGAGGTT 60.684 61.111 11.69 0.00 42.43 3.50
768 4735 2.539338 GCGGAAGTTGGTTCACGCA 61.539 57.895 12.60 0.00 46.02 5.24
770 4737 3.889171 GCGGAAGTTGGTTCACGCAAG 62.889 57.143 12.60 0.00 46.02 4.01
771 4738 0.310854 GGAAGTTGGTTCACGCAAGG 59.689 55.000 0.00 0.00 46.39 3.61
772 4739 1.305201 GAAGTTGGTTCACGCAAGGA 58.695 50.000 0.00 0.00 46.39 3.36
776 4743 2.494073 AGTTGGTTCACGCAAGGAAAAA 59.506 40.909 0.00 0.00 46.39 1.94
779 4746 1.679153 GGTTCACGCAAGGAAAAAGGA 59.321 47.619 0.00 0.00 46.39 3.36
780 4747 2.296190 GGTTCACGCAAGGAAAAAGGAT 59.704 45.455 0.00 0.00 46.39 3.24
781 4748 3.565516 GTTCACGCAAGGAAAAAGGATC 58.434 45.455 0.00 0.00 46.39 3.36
783 4750 1.135689 CACGCAAGGAAAAAGGATCCG 60.136 52.381 5.98 0.00 42.03 4.18
784 4751 0.451783 CGCAAGGAAAAAGGATCCGG 59.548 55.000 5.98 0.00 42.03 5.14
785 4752 0.173481 GCAAGGAAAAAGGATCCGGC 59.827 55.000 5.98 0.00 42.03 6.13
793 4760 3.385193 AAAAGGATCCGGCAAAAACAG 57.615 42.857 5.98 0.00 0.00 3.16
824 4791 4.342951 TCCCGTAGATATGACGAAAATGGT 59.657 41.667 8.06 0.00 42.98 3.55
825 4792 5.054477 CCCGTAGATATGACGAAAATGGTT 58.946 41.667 8.06 0.00 42.98 3.67
834 4801 1.000717 ACGAAAATGGTTCGGGCTTTG 60.001 47.619 12.55 0.00 45.34 2.77
838 4805 1.535204 AATGGTTCGGGCTTTGCAGG 61.535 55.000 0.00 0.00 0.00 4.85
844 4811 2.360191 GGGCTTTGCAGGATCCCA 59.640 61.111 8.55 0.00 36.96 4.37
846 4813 0.904394 GGGCTTTGCAGGATCCCAAA 60.904 55.000 8.55 11.71 36.96 3.28
847 4814 0.975887 GGCTTTGCAGGATCCCAAAA 59.024 50.000 8.55 6.05 31.29 2.44
848 4815 1.347378 GGCTTTGCAGGATCCCAAAAA 59.653 47.619 8.55 5.68 31.29 1.94
873 4840 3.740115 ACGGGATGATCGATTTTTAGGG 58.260 45.455 0.00 0.00 0.00 3.53
880 4847 7.497249 GGGATGATCGATTTTTAGGGATCTATG 59.503 40.741 0.00 0.00 36.96 2.23
881 4848 7.011857 GGATGATCGATTTTTAGGGATCTATGC 59.988 40.741 0.00 0.00 36.96 3.14
882 4849 6.768483 TGATCGATTTTTAGGGATCTATGCA 58.232 36.000 0.00 0.00 36.96 3.96
901 4868 0.240945 AGCTGAAAAATTCGCCCACG 59.759 50.000 0.00 0.00 42.01 4.94
912 4879 2.743538 GCCCACGACCCGTAAACC 60.744 66.667 0.00 0.00 38.32 3.27
913 4880 2.432972 CCCACGACCCGTAAACCG 60.433 66.667 0.00 0.00 38.32 4.44
935 4902 2.876550 GGCCATCCGAAATGGTTACTAC 59.123 50.000 15.51 1.64 41.17 2.73
950 4958 7.395190 TGGTTACTACTATGCTTTAACTCGA 57.605 36.000 0.00 0.00 0.00 4.04
959 4967 3.766151 TGCTTTAACTCGATCGTAGGTG 58.234 45.455 15.94 4.39 0.00 4.00
971 4979 1.200483 CGTAGGTGTAGCATTGCTCG 58.800 55.000 15.81 6.85 40.44 5.03
979 4987 5.696724 AGGTGTAGCATTGCTCGTATTTATC 59.303 40.000 15.81 0.00 40.44 1.75
1000 5011 6.652205 ATCCCATTACTACTCCCTTCAAAA 57.348 37.500 0.00 0.00 0.00 2.44
1035 5046 7.334574 AGATCGTTACGATGTTATATTGTGC 57.665 36.000 25.31 5.82 47.00 4.57
1111 5122 1.266867 TAGTTGGTTCCCCGCCTACC 61.267 60.000 0.00 0.00 33.32 3.18
1140 5158 0.899720 CGTAGCTAGGAACCCACCAA 59.100 55.000 7.70 0.00 0.00 3.67
1173 5199 5.667466 CGTAATTAAGCAGGTTTCCTCCTA 58.333 41.667 0.00 0.00 35.87 2.94
1174 5200 5.522824 CGTAATTAAGCAGGTTTCCTCCTAC 59.477 44.000 0.00 0.00 35.87 3.18
1175 5201 3.604875 TTAAGCAGGTTTCCTCCTACG 57.395 47.619 0.00 0.00 35.87 3.51
1212 5238 7.587028 GCTCATAAAGTCATCAGTACGTACTAC 59.413 40.741 26.95 20.57 34.13 2.73
1454 5484 0.620700 GTACCCCACCTGGATGGACT 60.621 60.000 14.48 4.33 43.02 3.85
1469 5499 4.330074 GGATGGACTACTTCACATTTGTCG 59.670 45.833 0.00 0.00 0.00 4.35
1561 5591 2.491022 CGCCCTCCTCGACCCTAAG 61.491 68.421 0.00 0.00 0.00 2.18
1672 5705 1.215382 CATCAACTCCGACGGCTCA 59.785 57.895 9.66 0.00 0.00 4.26
1685 5718 1.204941 ACGGCTCAGCGAAATACTTCT 59.795 47.619 0.00 0.00 0.00 2.85
1715 5748 2.325082 CCGTTGTCAGAAAGGCCCG 61.325 63.158 0.00 0.00 0.00 6.13
1770 5803 2.434331 CTTCTCCGCCAACCCCAA 59.566 61.111 0.00 0.00 0.00 4.12
1819 5852 2.280186 CGATACGGCCTTGGCCTC 60.280 66.667 25.99 16.62 0.00 4.70
1839 5872 2.909965 GTTCACCAAAGCCGGCCA 60.910 61.111 26.15 0.00 0.00 5.36
1999 6038 1.066573 CAGATATGGACCCTCGATGCC 60.067 57.143 0.00 0.00 0.00 4.40
2074 6119 3.991051 CCCGACCATCGCCGCTAT 61.991 66.667 0.00 0.00 38.82 2.97
2084 6129 1.005037 CGCCGCTATGGGAAGCATA 60.005 57.895 0.00 0.00 42.91 3.14
2164 6209 2.420466 GATACTCGAACCCGGCCC 59.580 66.667 0.00 0.00 36.24 5.80
2197 6242 2.111384 GTTCAGAGCTACCATCCAGGA 58.889 52.381 0.00 0.00 41.22 3.86
2203 6248 0.249657 GCTACCATCCAGGAAGCTCG 60.250 60.000 3.84 0.00 41.22 5.03
2207 6252 2.759973 ATCCAGGAAGCTCGCGGA 60.760 61.111 6.13 0.00 0.00 5.54
2326 6371 0.939577 CATCGACGTGGATAAGGCCG 60.940 60.000 13.00 0.00 0.00 6.13
2347 6392 1.329256 ACTGCGTCTACTTCACCTGT 58.671 50.000 0.00 0.00 0.00 4.00
2373 6418 2.628178 TGCCAGGTTCCGACTATATCAG 59.372 50.000 0.00 0.00 0.00 2.90
2417 6462 2.749621 CCTCCAGAAATTTGGGAGTTCG 59.250 50.000 23.88 12.16 45.42 3.95
2465 6510 1.668919 GCGACAGACGAGACATTCCAA 60.669 52.381 0.00 0.00 45.77 3.53
2542 6588 6.208797 TGTGATCCTAGAGTTGGTATAATCGG 59.791 42.308 0.00 0.00 0.00 4.18
2560 6615 3.774734 TCGGTGGATGTGCTATACCTAT 58.225 45.455 0.00 0.00 0.00 2.57
2604 6661 1.815003 CTTGAGGCCATGTTCTGTTCC 59.185 52.381 5.01 0.00 0.00 3.62
2637 6694 5.824097 TGTTTCCAAAGGTAACCACTCTAAC 59.176 40.000 3.58 0.00 33.05 2.34
2682 6739 8.181904 TCTGCATCAATTATTTCCCCTTTATC 57.818 34.615 0.00 0.00 0.00 1.75
2730 6793 5.126061 ACATAAACTTACCCTCGACGTACAT 59.874 40.000 0.00 0.00 0.00 2.29
2732 6795 5.643379 AAACTTACCCTCGACGTACATAA 57.357 39.130 0.00 0.00 0.00 1.90
2742 6805 6.965500 CCCTCGACGTACATAATCATACATAC 59.035 42.308 0.00 0.00 0.00 2.39
2767 6830 4.974368 TGAAAAATGACACAAACCGACT 57.026 36.364 0.00 0.00 0.00 4.18
2792 6855 2.737783 CAACTTGCGTTTCGGGTACATA 59.262 45.455 0.00 0.00 0.00 2.29
2840 6903 0.824595 AAACACTGCATGCCAGCTGA 60.825 50.000 17.39 0.00 45.78 4.26
2847 6910 4.415150 ATGCCAGCTGACCCACGG 62.415 66.667 17.39 0.00 0.00 4.94
2940 7003 0.179000 CGGCCAGCCAGAATCTAACT 59.821 55.000 9.78 0.00 35.37 2.24
2950 7013 4.081087 GCCAGAATCTAACTAAGGGTGACA 60.081 45.833 0.00 0.00 0.00 3.58
2958 7021 1.623811 ACTAAGGGTGACAAGTCGCAT 59.376 47.619 14.86 4.18 41.60 4.73
2972 7035 2.679837 AGTCGCATGAACCATTTGCTAG 59.320 45.455 0.00 0.00 34.23 3.42
3001 8097 3.134574 CCACCTGGTAGCTTGTGTTAA 57.865 47.619 0.00 0.00 0.00 2.01
3006 8102 3.502211 CCTGGTAGCTTGTGTTAACCAAG 59.498 47.826 22.40 22.40 41.75 3.61
3008 8104 2.817844 GGTAGCTTGTGTTAACCAAGGG 59.182 50.000 25.29 12.04 39.72 3.95
3010 8106 2.306847 AGCTTGTGTTAACCAAGGGTG 58.693 47.619 25.29 11.32 39.72 4.61
3012 8108 2.034179 GCTTGTGTTAACCAAGGGTGAC 59.966 50.000 25.29 13.00 39.72 3.67
3020 8117 0.991355 ACCAAGGGTGACAGGTCCAA 60.991 55.000 0.00 0.00 32.98 3.53
3021 8118 0.537371 CCAAGGGTGACAGGTCCAAC 60.537 60.000 0.00 0.00 0.00 3.77
3046 8143 6.751514 TTCGCATATGAGTTGTTATGGTTT 57.248 33.333 6.97 0.00 0.00 3.27
3070 8167 3.751175 CGCCTTATCACTTGGACAAAAGA 59.249 43.478 0.00 0.00 0.00 2.52
3073 8170 5.415701 GCCTTATCACTTGGACAAAAGATGA 59.584 40.000 8.35 1.70 0.00 2.92
3097 8194 4.431661 TGCGAAAACATGTGCATATGAA 57.568 36.364 27.77 0.00 31.31 2.57
3123 8221 8.734386 ACATCTGACCATTTGAATTCTAGTTTC 58.266 33.333 7.05 0.00 0.00 2.78
3179 8277 1.195115 TTTCAGATAGCCAGCCGACT 58.805 50.000 0.00 0.00 0.00 4.18
3190 8288 1.028905 CAGCCGACTGGGAAAAACAA 58.971 50.000 0.00 0.00 40.48 2.83
3248 8346 7.574496 TGCAATGCACAAATTTAGATTCAAAC 58.426 30.769 2.72 0.00 31.71 2.93
3251 8349 8.723311 CAATGCACAAATTTAGATTCAAACCAT 58.277 29.630 0.00 0.00 0.00 3.55
3318 8424 0.036388 GCAGGTTGCAGTGGCTAGTA 60.036 55.000 0.00 0.00 44.26 1.82
3321 8427 1.137086 AGGTTGCAGTGGCTAGTATCG 59.863 52.381 0.00 0.00 41.91 2.92
3346 8452 0.043310 GTGCGACACAACGTCTTGAC 60.043 55.000 3.50 0.00 42.98 3.18
3519 8628 2.165845 GTGTAGTGGCTAGTGTAGTGGG 59.834 54.545 0.00 0.00 0.00 4.61
3526 8635 2.100989 GCTAGTGTAGTGGGTAGCACT 58.899 52.381 0.00 0.00 43.55 4.40
3527 8636 3.285484 GCTAGTGTAGTGGGTAGCACTA 58.715 50.000 0.00 0.00 41.67 2.74
3586 8697 7.121272 AGTTAACGAAAATGTACTGAAACGTG 58.879 34.615 0.00 0.00 33.26 4.49
3589 8700 4.034742 ACGAAAATGTACTGAAACGTGCTT 59.965 37.500 0.00 0.00 0.00 3.91
3609 8720 5.130350 GCTTGGAATGCAAGTTATAGGGTA 58.870 41.667 15.64 0.00 36.91 3.69
3633 8744 7.775397 AGATTTGTGTCATTTTCCAAGTTTG 57.225 32.000 0.00 0.00 0.00 2.93
3642 8753 7.920151 TGTCATTTTCCAAGTTTGTGTATGAAG 59.080 33.333 0.00 0.00 0.00 3.02
3671 8784 7.928307 ACATCAAGTGCAAGTTTATGTATCT 57.072 32.000 7.71 0.00 41.05 1.98
3672 8785 7.978982 ACATCAAGTGCAAGTTTATGTATCTC 58.021 34.615 7.71 0.00 41.05 2.75
3826 8939 0.528470 CGAGCTTCTTCTTCCTCGGT 59.472 55.000 0.00 0.00 42.37 4.69
3874 8987 6.902771 TTTATTTTAGTACCTGGCAAAGCA 57.097 33.333 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.156736 CGAAACAGATCCCGCAAACT 58.843 50.000 0.00 0.00 0.00 2.66
1 2 0.872388 ACGAAACAGATCCCGCAAAC 59.128 50.000 0.00 0.00 0.00 2.93
4 5 2.032634 GCACGAAACAGATCCCGCA 61.033 57.895 0.00 0.00 0.00 5.69
17 3984 2.669569 GCAAGGCTTCCAGCACGA 60.670 61.111 0.00 0.00 44.75 4.35
63 4030 4.989044 TCATATGCAAGCACTTGTCAATG 58.011 39.130 11.77 11.59 42.31 2.82
124 4091 8.198807 TGGATGTGATGAACTAGTATGATGAT 57.801 34.615 0.00 0.00 0.00 2.45
134 4101 7.943079 ACATGATTTTGGATGTGATGAACTA 57.057 32.000 0.00 0.00 31.47 2.24
158 4125 2.028476 ACTTGCTACCTCGTATGTTGCA 60.028 45.455 6.71 6.71 41.46 4.08
159 4126 2.618053 ACTTGCTACCTCGTATGTTGC 58.382 47.619 0.00 0.00 35.47 4.17
175 4142 4.148696 CACGCATTTGAAAGGCTAAACTTG 59.851 41.667 12.86 0.00 0.00 3.16
178 4145 3.896122 TCACGCATTTGAAAGGCTAAAC 58.104 40.909 12.86 0.00 0.00 2.01
255 4222 1.286354 TGTTCGATGAAACGTCCGGC 61.286 55.000 0.00 0.00 34.70 6.13
261 4228 3.849708 TCTATCACGTGTTCGATGAAACG 59.150 43.478 16.51 0.00 41.64 3.60
264 4231 3.422655 CGTCTATCACGTGTTCGATGAA 58.577 45.455 16.51 0.00 44.07 2.57
280 4247 1.073722 ACTCCACCGGTCACGTCTA 59.926 57.895 2.59 0.00 38.78 2.59
283 4250 3.612681 CCACTCCACCGGTCACGT 61.613 66.667 2.59 0.00 38.78 4.49
290 4257 2.233605 TTATCACCGCCACTCCACCG 62.234 60.000 0.00 0.00 0.00 4.94
305 4272 1.446366 GGCCACGACCTCCCTTATC 59.554 63.158 0.00 0.00 0.00 1.75
333 4300 3.011517 GGCTGGGCTCCTTCTCCA 61.012 66.667 0.00 0.00 0.00 3.86
357 4324 0.809385 CGAGGAAGAAGGTACTCGCA 59.191 55.000 0.00 0.00 44.90 5.10
488 4455 1.003839 ATCGTTCAAGAGGGCGCAA 60.004 52.632 10.83 0.00 0.00 4.85
536 4503 3.192922 CTAAACCTTCCGCCGCCG 61.193 66.667 0.00 0.00 0.00 6.46
537 4504 2.822701 CCTAAACCTTCCGCCGCC 60.823 66.667 0.00 0.00 0.00 6.13
541 4508 2.822701 CGCCCCTAAACCTTCCGC 60.823 66.667 0.00 0.00 0.00 5.54
542 4509 2.124860 CCGCCCCTAAACCTTCCG 60.125 66.667 0.00 0.00 0.00 4.30
602 4569 2.480555 CGCAACCTCCAATGTCGC 59.519 61.111 0.00 0.00 0.00 5.19
621 4588 1.302752 TGGCCCATATCATGCGCTC 60.303 57.895 9.73 0.00 34.59 5.03
622 4589 1.601759 GTGGCCCATATCATGCGCT 60.602 57.895 9.73 0.00 34.59 5.92
641 4608 4.221703 AGATGAAGTACTCACAACCTCCAG 59.778 45.833 0.00 0.00 36.69 3.86
648 4615 5.680619 ACAAACCAGATGAAGTACTCACAA 58.319 37.500 0.00 0.00 36.69 3.33
662 4629 0.106918 AGTGCCGGAAACAAACCAGA 60.107 50.000 5.05 0.00 0.00 3.86
668 4635 2.203084 TCGCAGTGCCGGAAACAA 60.203 55.556 5.05 0.00 0.00 2.83
679 4646 4.148825 GATGTCCGGCCTCGCAGT 62.149 66.667 0.00 0.00 34.56 4.40
689 4656 1.141881 CCTCCAACCTCGATGTCCG 59.858 63.158 0.00 0.00 40.25 4.79
695 4662 0.970937 AATCTCGCCTCCAACCTCGA 60.971 55.000 0.00 0.00 0.00 4.04
702 4669 2.892640 CCGTCAATCTCGCCTCCA 59.107 61.111 0.00 0.00 0.00 3.86
728 4695 1.741770 CTTCCGTTTCCGCCTCCTG 60.742 63.158 0.00 0.00 0.00 3.86
729 4696 2.663196 CTTCCGTTTCCGCCTCCT 59.337 61.111 0.00 0.00 0.00 3.69
738 4705 4.629523 TTCCGCCCGCTTCCGTTT 62.630 61.111 0.00 0.00 0.00 3.60
742 4709 3.431725 CAACTTCCGCCCGCTTCC 61.432 66.667 0.00 0.00 0.00 3.46
751 4718 0.041312 CTTGCGTGAACCAACTTCCG 60.041 55.000 0.00 0.00 0.00 4.30
768 4735 2.302587 TTGCCGGATCCTTTTTCCTT 57.697 45.000 5.05 0.00 0.00 3.36
770 4737 3.064207 GTTTTTGCCGGATCCTTTTTCC 58.936 45.455 5.05 0.00 0.00 3.13
771 4738 3.723260 TGTTTTTGCCGGATCCTTTTTC 58.277 40.909 5.05 0.00 0.00 2.29
772 4739 3.494223 CCTGTTTTTGCCGGATCCTTTTT 60.494 43.478 5.05 0.00 0.00 1.94
776 4743 0.611896 CCCTGTTTTTGCCGGATCCT 60.612 55.000 5.05 0.00 0.00 3.24
779 4746 1.241315 CGTCCCTGTTTTTGCCGGAT 61.241 55.000 5.05 0.00 0.00 4.18
780 4747 1.894756 CGTCCCTGTTTTTGCCGGA 60.895 57.895 5.05 0.00 0.00 5.14
781 4748 2.642700 CGTCCCTGTTTTTGCCGG 59.357 61.111 0.00 0.00 0.00 6.13
783 4750 0.031585 GAACCGTCCCTGTTTTTGCC 59.968 55.000 0.00 0.00 0.00 4.52
784 4751 0.031585 GGAACCGTCCCTGTTTTTGC 59.968 55.000 0.00 0.00 38.08 3.68
803 4770 5.107989 CGAACCATTTTCGTCATATCTACGG 60.108 44.000 7.16 0.00 40.68 4.02
805 4772 5.176958 CCCGAACCATTTTCGTCATATCTAC 59.823 44.000 5.75 0.00 40.04 2.59
824 4791 1.378514 GGATCCTGCAAAGCCCGAA 60.379 57.895 3.84 0.00 0.00 4.30
825 4792 2.272146 GGATCCTGCAAAGCCCGA 59.728 61.111 3.84 0.00 0.00 5.14
846 4813 8.349983 CCTAAAAATCGATCATCCCGTAATTTT 58.650 33.333 0.00 0.47 30.21 1.82
847 4814 7.040686 CCCTAAAAATCGATCATCCCGTAATTT 60.041 37.037 0.00 0.00 0.00 1.82
848 4815 6.430000 CCCTAAAAATCGATCATCCCGTAATT 59.570 38.462 0.00 0.00 0.00 1.40
849 4816 5.938125 CCCTAAAAATCGATCATCCCGTAAT 59.062 40.000 0.00 0.00 0.00 1.89
860 4827 5.645497 GCTGCATAGATCCCTAAAAATCGAT 59.355 40.000 0.00 0.00 0.00 3.59
861 4828 4.997395 GCTGCATAGATCCCTAAAAATCGA 59.003 41.667 0.00 0.00 0.00 3.59
862 4829 4.999950 AGCTGCATAGATCCCTAAAAATCG 59.000 41.667 1.02 0.00 0.00 3.34
869 4836 5.372343 TTTTTCAGCTGCATAGATCCCTA 57.628 39.130 9.47 0.00 0.00 3.53
870 4837 3.939740 TTTTCAGCTGCATAGATCCCT 57.060 42.857 9.47 0.00 0.00 4.20
873 4840 4.674211 GCGAATTTTTCAGCTGCATAGATC 59.326 41.667 9.47 2.69 0.00 2.75
880 4847 0.038343 TGGGCGAATTTTTCAGCTGC 60.038 50.000 9.47 0.00 32.49 5.25
881 4848 1.701704 GTGGGCGAATTTTTCAGCTG 58.298 50.000 7.63 7.63 32.49 4.24
882 4849 0.240945 CGTGGGCGAATTTTTCAGCT 59.759 50.000 0.00 0.00 41.33 4.24
913 4880 1.029681 GTAACCATTTCGGATGGCCC 58.970 55.000 15.79 3.88 42.82 5.80
919 4886 5.864418 AGCATAGTAGTAACCATTTCGGA 57.136 39.130 0.00 0.00 38.63 4.55
928 4895 7.854916 ACGATCGAGTTAAAGCATAGTAGTAAC 59.145 37.037 24.34 0.00 0.00 2.50
935 4902 5.625721 CACCTACGATCGAGTTAAAGCATAG 59.374 44.000 24.34 8.50 0.00 2.23
950 4958 2.543861 CGAGCAATGCTACACCTACGAT 60.544 50.000 8.12 0.00 39.88 3.73
959 4967 4.994852 TGGGATAAATACGAGCAATGCTAC 59.005 41.667 8.12 0.90 39.88 3.58
971 4979 8.877195 TGAAGGGAGTAGTAATGGGATAAATAC 58.123 37.037 0.00 0.00 0.00 1.89
1012 5023 6.087159 TCGCACAATATAACATCGTAACGATC 59.913 38.462 0.00 0.00 45.19 3.69
1018 5029 3.976306 CCGTCGCACAATATAACATCGTA 59.024 43.478 0.00 0.00 0.00 3.43
1031 5042 2.034532 TACTCCCTCCGTCGCACA 59.965 61.111 0.00 0.00 0.00 4.57
1035 5046 2.667473 AAATTGTACTCCCTCCGTCG 57.333 50.000 0.00 0.00 0.00 5.12
1140 5158 4.090930 CCTGCTTAATTACGCGCGTATATT 59.909 41.667 39.48 34.92 0.00 1.28
1173 5199 1.423721 TATGAGCTCGCGTACGTCGT 61.424 55.000 23.95 14.64 42.13 4.34
1174 5200 0.315625 TTATGAGCTCGCGTACGTCG 60.316 55.000 17.90 19.60 41.18 5.12
1175 5201 1.774085 CTTTATGAGCTCGCGTACGTC 59.226 52.381 17.90 6.50 41.18 4.34
1303 5333 3.736433 CGATGCTCCTCAAGAGATCGTTT 60.736 47.826 9.45 0.00 46.50 3.60
1305 5335 1.336440 CGATGCTCCTCAAGAGATCGT 59.664 52.381 9.45 0.00 46.50 3.73
1306 5336 1.335780 CCGATGCTCCTCAAGAGATCG 60.336 57.143 10.28 10.28 46.50 3.69
1454 5484 2.614481 GGAGGGCGACAAATGTGAAGTA 60.614 50.000 0.00 0.00 0.00 2.24
1631 5661 4.101645 CGAAGGGACTAGGATAGAGGAA 57.898 50.000 0.00 0.00 42.77 3.36
1672 5705 1.535437 CCCGCGTAGAAGTATTTCGCT 60.535 52.381 4.92 0.00 39.40 4.93
1700 5733 1.150536 AAGCGGGCCTTTCTGACAA 59.849 52.632 0.84 0.00 0.00 3.18
1701 5734 1.600636 CAAGCGGGCCTTTCTGACA 60.601 57.895 0.84 0.00 0.00 3.58
1702 5735 2.982744 GCAAGCGGGCCTTTCTGAC 61.983 63.158 0.84 0.00 0.00 3.51
1703 5736 2.672996 GCAAGCGGGCCTTTCTGA 60.673 61.111 0.84 0.00 0.00 3.27
1810 5843 3.423154 GTGAACGCGAGGCCAAGG 61.423 66.667 15.93 0.00 0.00 3.61
1819 5852 4.383602 CCGGCTTTGGTGAACGCG 62.384 66.667 3.53 3.53 0.00 6.01
2023 6068 2.530497 GCACTTGACGAACGGCACA 61.530 57.895 1.14 0.00 29.74 4.57
2074 6119 2.722094 GTGAACACCATATGCTTCCCA 58.278 47.619 0.00 0.00 0.00 4.37
2207 6252 3.382832 CTTCCTCCAGCGTCGGGT 61.383 66.667 0.00 0.00 0.00 5.28
2347 6392 1.496060 AGTCGGAACCTGGCATGATA 58.504 50.000 0.00 0.00 0.00 2.15
2359 6404 3.075148 CTCTCCGCTGATATAGTCGGAA 58.925 50.000 11.31 4.55 46.64 4.30
2373 6418 1.214062 CACTCCACAGACTCTCCGC 59.786 63.158 0.00 0.00 0.00 5.54
2417 6462 4.240049 GACACCGGTCTTCACGTC 57.760 61.111 2.59 4.07 40.99 4.34
2465 6510 2.636830 CCACTCGAGCCAATCTGAATT 58.363 47.619 13.61 0.00 0.00 2.17
2542 6588 6.159988 GTGAGAATAGGTATAGCACATCCAC 58.840 44.000 4.48 5.95 0.00 4.02
2560 6615 1.623311 TGAGGAAATCGCAGGTGAGAA 59.377 47.619 0.00 0.00 0.00 2.87
2637 6694 1.522569 GGATCCACTCAACCCCTCG 59.477 63.158 6.95 0.00 0.00 4.63
2643 6700 0.615331 TGCAGAGGGATCCACTCAAC 59.385 55.000 23.98 17.71 37.43 3.18
2716 6773 4.823442 TGTATGATTATGTACGTCGAGGGT 59.177 41.667 10.27 2.04 0.00 4.34
2718 6775 7.480855 GTGTATGTATGATTATGTACGTCGAGG 59.519 40.741 3.03 3.03 0.00 4.63
2742 6805 5.004345 GTCGGTTTGTGTCATTTTTCAAGTG 59.996 40.000 0.00 0.00 0.00 3.16
2792 6855 7.063074 CGGAGAGTTAACGAAAAATGTACTGAT 59.937 37.037 0.00 0.00 0.00 2.90
2840 6903 1.379044 CGTAGGTAGGACCGTGGGT 60.379 63.158 0.00 0.00 44.90 4.51
2847 6910 0.813821 GACCCACACGTAGGTAGGAC 59.186 60.000 4.23 0.00 36.17 3.85
2940 7003 1.621317 TCATGCGACTTGTCACCCTTA 59.379 47.619 1.59 0.00 0.00 2.69
2950 7013 1.888512 AGCAAATGGTTCATGCGACTT 59.111 42.857 0.00 0.00 44.60 3.01
2958 7021 2.584835 AGTGCCTAGCAAATGGTTCA 57.415 45.000 0.00 0.00 41.47 3.18
3001 8097 0.991355 TTGGACCTGTCACCCTTGGT 60.991 55.000 0.00 0.00 35.62 3.67
3006 8102 1.605753 GAAAGTTGGACCTGTCACCC 58.394 55.000 0.00 0.00 0.00 4.61
3008 8104 0.586802 GCGAAAGTTGGACCTGTCAC 59.413 55.000 0.00 0.00 0.00 3.67
3010 8106 1.523758 ATGCGAAAGTTGGACCTGTC 58.476 50.000 0.00 0.00 0.00 3.51
3012 8108 3.270027 TCATATGCGAAAGTTGGACCTG 58.730 45.455 0.00 0.00 0.00 4.00
3020 8117 5.880332 ACCATAACAACTCATATGCGAAAGT 59.120 36.000 0.00 0.00 0.00 2.66
3021 8118 6.363577 ACCATAACAACTCATATGCGAAAG 57.636 37.500 0.00 0.00 0.00 2.62
3046 8143 0.323302 TGTCCAAGTGATAAGGCGCA 59.677 50.000 10.83 0.00 0.00 6.09
3070 8167 4.635833 TGCACATGTTTTCGCATATCAT 57.364 36.364 4.58 0.00 0.00 2.45
3097 8194 8.641498 AAACTAGAATTCAAATGGTCAGATGT 57.359 30.769 8.44 0.00 0.00 3.06
3123 8221 7.275785 CGTGAATGCTTTTGACATTGTTAAAG 58.724 34.615 15.51 15.51 37.85 1.85
3179 8277 4.340950 GGTCTCTCAACATTGTTTTTCCCA 59.659 41.667 0.00 0.00 0.00 4.37
3190 8288 2.037772 GTGTGAGTGGGTCTCTCAACAT 59.962 50.000 1.91 0.00 44.62 2.71
3318 8424 2.885644 GTGTCGCACGCATCCGAT 60.886 61.111 0.00 0.00 38.29 4.18
3321 8427 2.173382 GTTGTGTCGCACGCATCC 59.827 61.111 3.88 0.00 38.53 3.51
3477 8586 6.474630 ACACCACCCGTTCTTATATGTTTAA 58.525 36.000 0.00 0.00 0.00 1.52
3493 8602 0.249398 CACTAGCCACTACACCACCC 59.751 60.000 0.00 0.00 0.00 4.61
3589 8700 6.763715 ATCTACCCTATAACTTGCATTCCA 57.236 37.500 0.00 0.00 0.00 3.53
3609 8720 7.278424 CACAAACTTGGAAAATGACACAAATCT 59.722 33.333 0.00 0.00 0.00 2.40
3625 8736 7.022055 TGTACAACTTCATACACAAACTTGG 57.978 36.000 0.00 0.00 0.00 3.61
3633 8744 6.073276 TGCACTTGATGTACAACTTCATACAC 60.073 38.462 0.00 0.00 34.24 2.90
3642 8753 7.138736 ACATAAACTTGCACTTGATGTACAAC 58.861 34.615 0.00 0.00 34.56 3.32
3696 8809 9.734984 ACATTTGCCTAACTAAACACTAGTATT 57.265 29.630 0.00 0.00 0.00 1.89
3699 8812 9.216117 CTTACATTTGCCTAACTAAACACTAGT 57.784 33.333 0.00 0.00 0.00 2.57
3700 8813 8.665685 CCTTACATTTGCCTAACTAAACACTAG 58.334 37.037 0.00 0.00 0.00 2.57
3780 8893 0.951558 GAGTGCAAAAGGAAGGCGAA 59.048 50.000 0.00 0.00 0.00 4.70
3782 8895 0.954452 AAGAGTGCAAAAGGAAGGCG 59.046 50.000 0.00 0.00 0.00 5.52
3826 8939 5.651530 TCTACGCCAACATTTTGTTTTCAA 58.348 33.333 0.00 0.00 38.77 2.69


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

AutoCloner maintained by Alex Coulton.