Multiple sequence alignment - TraesCS6D01G060000

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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 TraesCS6D01G060000 chr6D 100.000 3352 0 0 1 3352 28152867 28156218 0.000000e+00 6191.0
1 TraesCS6D01G060000 chr6D 89.469 1225 105 11 1154 2364 28266070 28264856 0.000000e+00 1526.0
2 TraesCS6D01G060000 chr6D 92.424 726 50 3 1 726 351957682 351956962 0.000000e+00 1031.0
3 TraesCS6D01G060000 chr6B 90.068 2507 147 38 903 3350 52138263 52135800 0.000000e+00 3157.0
4 TraesCS6D01G060000 chr6B 89.188 2118 128 38 928 3011 52075569 52077619 0.000000e+00 2549.0
5 TraesCS6D01G060000 chr6B 81.481 297 32 12 3057 3349 52077622 52077899 4.350000e-54 222.0
6 TraesCS6D01G060000 chr6B 86.111 180 18 4 912 1091 52058141 52058313 1.590000e-43 187.0
7 TraesCS6D01G060000 chr6A 88.051 2494 179 56 903 3352 29806976 29804558 0.000000e+00 2844.0
8 TraesCS6D01G060000 chr6A 90.334 838 55 5 1531 2364 29755278 29756093 0.000000e+00 1075.0
9 TraesCS6D01G060000 chr6A 84.224 393 26 13 938 1324 29716556 29716918 1.910000e-92 350.0
10 TraesCS6D01G060000 chr6A 89.352 216 21 2 1322 1537 29737748 29737961 1.530000e-68 270.0
11 TraesCS6D01G060000 chr6A 91.429 105 9 0 3245 3349 29811056 29810952 9.690000e-31 145.0
12 TraesCS6D01G060000 chr6A 91.429 105 9 0 3245 3349 29812214 29812110 9.690000e-31 145.0
13 TraesCS6D01G060000 chr6A 93.846 65 3 1 858 921 29807052 29806988 2.750000e-16 97.1
14 TraesCS6D01G060000 chr6A 100.000 29 0 0 767 795 29807077 29807049 2.000000e-03 54.7
15 TraesCS6D01G060000 chr7D 93.260 727 47 2 1 727 599795613 599796337 0.000000e+00 1070.0
16 TraesCS6D01G060000 chr2D 92.926 721 45 6 9 726 557284122 557283405 0.000000e+00 1044.0
17 TraesCS6D01G060000 chr2D 92.403 724 52 3 9 730 48383772 48383050 0.000000e+00 1029.0
18 TraesCS6D01G060000 chr5B 92.055 730 50 5 1 728 237141053 237141776 0.000000e+00 1020.0
19 TraesCS6D01G060000 chr4A 91.621 728 54 6 1 726 742814746 742815468 0.000000e+00 1000.0
20 TraesCS6D01G060000 chr4A 91.472 727 56 4 1 726 108417293 108416572 0.000000e+00 994.0
21 TraesCS6D01G060000 chr3B 91.245 731 57 4 1 726 752238963 752238235 0.000000e+00 989.0
22 TraesCS6D01G060000 chr5D 91.108 731 61 4 1 729 379095356 379094628 0.000000e+00 987.0
23 TraesCS6D01G060000 chrUn 91.429 105 9 0 3245 3349 71736338 71736234 9.690000e-31 145.0
24 TraesCS6D01G060000 chrUn 91.429 105 9 0 3245 3349 365837336 365837440 9.690000e-31 145.0
25 TraesCS6D01G060000 chrUn 91.429 105 9 0 3245 3349 377995349 377995453 9.690000e-31 145.0
26 TraesCS6D01G060000 chr4D 90.000 70 5 1 2478 2545 220348109 220348178 4.610000e-14 89.8
27 TraesCS6D01G060000 chr4B 91.045 67 4 1 2481 2545 315722284 315722218 4.610000e-14 89.8
28 TraesCS6D01G060000 chr5A 86.076 79 7 2 2460 2538 631618815 631618741 7.710000e-12 82.4


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 TraesCS6D01G060000 chr6D 28152867 28156218 3351 False 6191.00 6191 100.0000 1 3352 1 chr6D.!!$F1 3351
1 TraesCS6D01G060000 chr6D 28264856 28266070 1214 True 1526.00 1526 89.4690 1154 2364 1 chr6D.!!$R1 1210
2 TraesCS6D01G060000 chr6D 351956962 351957682 720 True 1031.00 1031 92.4240 1 726 1 chr6D.!!$R2 725
3 TraesCS6D01G060000 chr6B 52135800 52138263 2463 True 3157.00 3157 90.0680 903 3350 1 chr6B.!!$R1 2447
4 TraesCS6D01G060000 chr6B 52075569 52077899 2330 False 1385.50 2549 85.3345 928 3349 2 chr6B.!!$F2 2421
5 TraesCS6D01G060000 chr6A 29755278 29756093 815 False 1075.00 1075 90.3340 1531 2364 1 chr6A.!!$F3 833
6 TraesCS6D01G060000 chr6A 29804558 29812214 7656 True 657.16 2844 92.9510 767 3352 5 chr6A.!!$R1 2585
7 TraesCS6D01G060000 chr7D 599795613 599796337 724 False 1070.00 1070 93.2600 1 727 1 chr7D.!!$F1 726
8 TraesCS6D01G060000 chr2D 557283405 557284122 717 True 1044.00 1044 92.9260 9 726 1 chr2D.!!$R2 717
9 TraesCS6D01G060000 chr2D 48383050 48383772 722 True 1029.00 1029 92.4030 9 730 1 chr2D.!!$R1 721
10 TraesCS6D01G060000 chr5B 237141053 237141776 723 False 1020.00 1020 92.0550 1 728 1 chr5B.!!$F1 727
11 TraesCS6D01G060000 chr4A 742814746 742815468 722 False 1000.00 1000 91.6210 1 726 1 chr4A.!!$F1 725
12 TraesCS6D01G060000 chr4A 108416572 108417293 721 True 994.00 994 91.4720 1 726 1 chr4A.!!$R1 725
13 TraesCS6D01G060000 chr3B 752238235 752238963 728 True 989.00 989 91.2450 1 726 1 chr3B.!!$R1 725
14 TraesCS6D01G060000 chr5D 379094628 379095356 728 True 987.00 987 91.1080 1 729 1 chr5D.!!$R1 728

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
797 5169 0.249868 TCCTCCGTGTGCAAGTTCTG 60.250 55.0 0.00 0.00 0.00 3.02 F
849 5221 0.320050 TGCTGCGTATGTGACCTTCA 59.680 50.0 0.00 0.00 0.00 3.02 F
1666 6095 0.038166 TGACACCCTGGGAAGCATTC 59.962 55.0 22.23 6.41 46.67 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 6076 0.038166 GAATGCTTCCCAGGGTGTCA 59.962 55.0 5.01 1.98 0.0 3.58 R
2065 6506 0.319211 CAAGCCGTACCAAGTCGACA 60.319 55.0 19.50 0.00 0.0 4.35 R
2932 7414 0.107508 CAGGCAGTGTACATCCAGGG 60.108 60.0 0.00 0.00 0.0 4.45 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
76 78 7.409697 TCTGCGAAATATTATCAAAGACAAGC 58.590 34.615 0.00 0.00 0.00 4.01
131 133 3.058914 ACAGAAACATTTGCTACTGACGC 60.059 43.478 0.00 0.00 0.00 5.19
187 190 2.492088 GGTTTCCTACAAGAACATGCCC 59.508 50.000 0.00 0.00 0.00 5.36
226 230 8.537728 TGAATAACCTTTATCCTCATTTGCAT 57.462 30.769 0.00 0.00 0.00 3.96
377 381 2.152016 GGGCTACACTCACAAAGAACC 58.848 52.381 0.00 0.00 0.00 3.62
391 395 0.321122 AGAACCGGAGCAGCTTCTTG 60.321 55.000 9.46 0.00 0.00 3.02
523 537 7.201496 CCTTTGCTACGTAACTTGGTATTACTG 60.201 40.741 0.00 0.00 31.53 2.74
614 632 6.267699 TCCTGTCCGTATGACTATCATCAATT 59.732 38.462 0.00 0.00 44.75 2.32
616 634 7.049799 TGTCCGTATGACTATCATCAATTCA 57.950 36.000 0.00 0.00 44.75 2.57
671 689 8.119226 GTCTACATATTTTGATGCACACTCTTC 58.881 37.037 0.00 0.00 0.00 2.87
730 748 3.381949 GCAACGGGTCATCTAGTGTATC 58.618 50.000 0.00 0.00 0.00 2.24
731 749 3.799232 GCAACGGGTCATCTAGTGTATCC 60.799 52.174 0.00 0.00 0.00 2.59
732 750 3.596940 ACGGGTCATCTAGTGTATCCT 57.403 47.619 0.00 0.00 0.00 3.24
733 751 4.719026 ACGGGTCATCTAGTGTATCCTA 57.281 45.455 0.00 0.00 0.00 2.94
734 752 5.057843 ACGGGTCATCTAGTGTATCCTAA 57.942 43.478 0.00 0.00 0.00 2.69
735 753 4.826183 ACGGGTCATCTAGTGTATCCTAAC 59.174 45.833 0.00 0.00 0.00 2.34
736 754 4.825634 CGGGTCATCTAGTGTATCCTAACA 59.174 45.833 0.00 0.00 0.00 2.41
737 755 5.301045 CGGGTCATCTAGTGTATCCTAACAA 59.699 44.000 0.00 0.00 0.00 2.83
738 756 6.515200 CGGGTCATCTAGTGTATCCTAACAAG 60.515 46.154 0.00 0.00 0.00 3.16
739 757 6.239345 GGGTCATCTAGTGTATCCTAACAAGG 60.239 46.154 0.00 0.00 0.00 3.61
740 758 6.239345 GGTCATCTAGTGTATCCTAACAAGGG 60.239 46.154 0.00 0.00 0.00 3.95
741 759 5.304614 TCATCTAGTGTATCCTAACAAGGGC 59.695 44.000 0.00 0.00 0.00 5.19
742 760 3.965347 TCTAGTGTATCCTAACAAGGGCC 59.035 47.826 0.00 0.00 0.00 5.80
743 761 2.557869 AGTGTATCCTAACAAGGGCCA 58.442 47.619 6.18 0.00 0.00 5.36
744 762 2.505819 AGTGTATCCTAACAAGGGCCAG 59.494 50.000 6.18 0.00 0.00 4.85
745 763 1.211949 TGTATCCTAACAAGGGCCAGC 59.788 52.381 6.18 0.00 0.00 4.85
746 764 0.843984 TATCCTAACAAGGGCCAGCC 59.156 55.000 6.18 0.00 0.00 4.85
759 777 4.697756 CAGCCCGTTCCCTCGCAA 62.698 66.667 0.00 0.00 0.00 4.85
760 778 3.948719 AGCCCGTTCCCTCGCAAA 61.949 61.111 0.00 0.00 0.00 3.68
761 779 2.981350 GCCCGTTCCCTCGCAAAA 60.981 61.111 0.00 0.00 0.00 2.44
762 780 2.557372 GCCCGTTCCCTCGCAAAAA 61.557 57.895 0.00 0.00 0.00 1.94
795 5167 0.586802 GTTCCTCCGTGTGCAAGTTC 59.413 55.000 0.00 0.00 0.00 3.01
796 5168 0.468226 TTCCTCCGTGTGCAAGTTCT 59.532 50.000 0.00 0.00 0.00 3.01
797 5169 0.249868 TCCTCCGTGTGCAAGTTCTG 60.250 55.000 0.00 0.00 0.00 3.02
798 5170 0.532862 CCTCCGTGTGCAAGTTCTGT 60.533 55.000 0.00 0.00 0.00 3.41
799 5171 1.270094 CCTCCGTGTGCAAGTTCTGTA 60.270 52.381 0.00 0.00 0.00 2.74
800 5172 2.479837 CTCCGTGTGCAAGTTCTGTAA 58.520 47.619 0.00 0.00 0.00 2.41
801 5173 3.067106 CTCCGTGTGCAAGTTCTGTAAT 58.933 45.455 0.00 0.00 0.00 1.89
802 5174 2.805671 TCCGTGTGCAAGTTCTGTAATG 59.194 45.455 0.00 0.00 0.00 1.90
803 5175 2.574322 CGTGTGCAAGTTCTGTAATGC 58.426 47.619 0.00 0.00 39.22 3.56
804 5176 2.224079 CGTGTGCAAGTTCTGTAATGCT 59.776 45.455 0.00 0.00 39.49 3.79
805 5177 3.558505 GTGTGCAAGTTCTGTAATGCTG 58.441 45.455 0.00 0.00 39.49 4.41
806 5178 2.030893 TGTGCAAGTTCTGTAATGCTGC 60.031 45.455 0.00 0.00 39.49 5.25
807 5179 2.227388 GTGCAAGTTCTGTAATGCTGCT 59.773 45.455 0.00 0.00 39.49 4.24
808 5180 2.886523 TGCAAGTTCTGTAATGCTGCTT 59.113 40.909 0.00 0.00 39.49 3.91
809 5181 3.318839 TGCAAGTTCTGTAATGCTGCTTT 59.681 39.130 0.00 3.33 39.49 3.51
810 5182 4.202141 TGCAAGTTCTGTAATGCTGCTTTT 60.202 37.500 6.08 0.20 39.49 2.27
811 5183 4.746611 GCAAGTTCTGTAATGCTGCTTTTT 59.253 37.500 6.08 0.00 35.93 1.94
834 5206 5.437289 TTTTTGAGTGGTCTGTAATGCTG 57.563 39.130 0.00 0.00 0.00 4.41
835 5207 2.099141 TGAGTGGTCTGTAATGCTGC 57.901 50.000 0.00 0.00 0.00 5.25
836 5208 1.002366 GAGTGGTCTGTAATGCTGCG 58.998 55.000 0.00 0.00 0.00 5.18
837 5209 0.321671 AGTGGTCTGTAATGCTGCGT 59.678 50.000 0.00 0.00 0.00 5.24
838 5210 1.548719 AGTGGTCTGTAATGCTGCGTA 59.451 47.619 0.00 0.00 0.00 4.42
839 5211 2.168521 AGTGGTCTGTAATGCTGCGTAT 59.831 45.455 0.00 0.00 0.00 3.06
840 5212 2.285220 GTGGTCTGTAATGCTGCGTATG 59.715 50.000 0.00 0.00 0.00 2.39
841 5213 2.093711 TGGTCTGTAATGCTGCGTATGT 60.094 45.455 0.00 0.00 0.00 2.29
842 5214 2.285220 GGTCTGTAATGCTGCGTATGTG 59.715 50.000 0.00 0.00 0.00 3.21
843 5215 3.186909 GTCTGTAATGCTGCGTATGTGA 58.813 45.455 0.00 0.00 0.00 3.58
844 5216 3.000322 GTCTGTAATGCTGCGTATGTGAC 60.000 47.826 0.00 0.00 0.00 3.67
845 5217 2.276201 TGTAATGCTGCGTATGTGACC 58.724 47.619 0.00 0.00 0.00 4.02
846 5218 2.093711 TGTAATGCTGCGTATGTGACCT 60.094 45.455 0.00 0.00 0.00 3.85
847 5219 2.113860 AATGCTGCGTATGTGACCTT 57.886 45.000 0.00 0.00 0.00 3.50
848 5220 1.656652 ATGCTGCGTATGTGACCTTC 58.343 50.000 0.00 0.00 0.00 3.46
849 5221 0.320050 TGCTGCGTATGTGACCTTCA 59.680 50.000 0.00 0.00 0.00 3.02
850 5222 1.270571 TGCTGCGTATGTGACCTTCAA 60.271 47.619 0.00 0.00 0.00 2.69
851 5223 1.128692 GCTGCGTATGTGACCTTCAAC 59.871 52.381 0.00 0.00 0.00 3.18
852 5224 2.412870 CTGCGTATGTGACCTTCAACA 58.587 47.619 0.00 0.00 0.00 3.33
853 5225 2.412870 TGCGTATGTGACCTTCAACAG 58.587 47.619 0.00 0.00 0.00 3.16
893 5265 0.447801 CCAGTCGATTTTTCCAGCCG 59.552 55.000 0.00 0.00 0.00 5.52
896 5268 0.727398 GTCGATTTTTCCAGCCGAGG 59.273 55.000 0.00 0.00 0.00 4.63
912 5315 2.613223 CCGAGGAGTTCAGGAGGTTTTC 60.613 54.545 0.00 0.00 0.00 2.29
965 5377 3.574396 TGAGGTTGTGAAGGACTACAGAG 59.426 47.826 0.00 0.00 32.47 3.35
1051 5470 2.979814 AACCAACCAAAACTTGCCTC 57.020 45.000 0.00 0.00 0.00 4.70
1069 5493 2.477825 CTCGTACTCCATCCAAGCATG 58.522 52.381 0.00 0.00 0.00 4.06
1070 5494 0.940126 CGTACTCCATCCAAGCATGC 59.060 55.000 10.51 10.51 0.00 4.06
1071 5495 1.743431 CGTACTCCATCCAAGCATGCA 60.743 52.381 21.98 0.00 0.00 3.96
1072 5496 2.579873 GTACTCCATCCAAGCATGCAT 58.420 47.619 21.98 4.57 0.00 3.96
1078 5502 0.851469 ATCCAAGCATGCATCTCCCT 59.149 50.000 21.98 0.00 0.00 4.20
1091 5515 4.037565 TGCATCTCCCTACGTTGTATGTAG 59.962 45.833 0.00 0.00 37.43 2.74
1160 5584 1.271325 TGATGATGGCGGACAACAAGT 60.271 47.619 0.00 0.00 35.38 3.16
1161 5585 1.398390 GATGATGGCGGACAACAAGTC 59.602 52.381 0.00 0.00 46.83 3.01
1372 5799 1.429825 CGCGAGATTCGACTCCACT 59.570 57.895 0.00 0.00 43.74 4.00
1382 5809 3.941657 GACTCCACTGAGGTGCGCC 62.942 68.421 8.71 8.71 43.29 6.53
1496 5923 1.153823 CTCCTGCACGACCCTTACG 60.154 63.158 0.00 0.00 0.00 3.18
1666 6095 0.038166 TGACACCCTGGGAAGCATTC 59.962 55.000 22.23 6.41 46.67 2.67
1715 6144 2.123251 GGGGAGATCGCTGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1717 6146 1.758514 GGGAGATCGCTGGAGGACA 60.759 63.158 0.00 0.00 0.00 4.02
1738 6167 4.717629 TCTGTCGAAGGCGTGCCG 62.718 66.667 5.02 0.00 41.95 5.69
1787 6220 1.009675 GCTGTGTGCGACAAACTGG 60.010 57.895 8.36 1.63 32.80 4.00
1789 6222 1.713937 CTGTGTGCGACAAACTGGCA 61.714 55.000 0.00 0.00 32.80 4.92
1809 6242 4.974989 GGTGTTCGCCGACGGGTT 62.975 66.667 17.22 0.00 40.63 4.11
1885 6318 1.372997 GCTGTCTTTCTCCGTCGCA 60.373 57.895 0.00 0.00 0.00 5.10
1955 6388 2.282251 ACCTGACGGAGCTCGACA 60.282 61.111 7.83 8.80 42.43 4.35
2029 6462 2.257207 TCGTTGGAGATCTGGAAGGTT 58.743 47.619 0.00 0.00 0.00 3.50
2046 6487 5.377478 GAAGGTTAGGGAAGATAATGGTGG 58.623 45.833 0.00 0.00 0.00 4.61
2065 6506 3.381983 TGGTCGCTGGAGCATCGT 61.382 61.111 0.00 0.00 45.17 3.73
2254 6695 5.220605 CGGAGGAATTTCTCGTTATGAAACC 60.221 44.000 7.68 0.00 36.43 3.27
2325 6771 0.320771 CAGAGGCACGGTGCTAAACT 60.321 55.000 29.92 19.39 44.28 2.66
2366 6812 4.909696 ATGAACAATCAACAACGGAACA 57.090 36.364 0.00 0.00 39.49 3.18
2432 6888 2.287308 CGATCCGGTTTCTGAGCTCTAG 60.287 54.545 16.19 10.75 0.00 2.43
2438 6894 2.615869 GTTTCTGAGCTCTAGGTGCTG 58.384 52.381 16.19 3.61 41.30 4.41
2439 6895 1.930251 TTCTGAGCTCTAGGTGCTGT 58.070 50.000 16.19 0.00 41.30 4.40
2440 6896 2.808906 TCTGAGCTCTAGGTGCTGTA 57.191 50.000 16.19 4.65 41.30 2.74
2441 6897 2.370349 TCTGAGCTCTAGGTGCTGTAC 58.630 52.381 16.19 3.35 41.30 2.90
2633 7102 0.249955 CGGCAAAAGCCAATTCCCAT 59.750 50.000 7.34 0.00 0.00 4.00
2769 7238 8.458843 GCAGTTGTAATTTGAAGCCTAGATTTA 58.541 33.333 0.00 0.00 0.00 1.40
2784 7253 5.710099 CCTAGATTTAACAGCTCCACCAAAA 59.290 40.000 0.00 0.00 0.00 2.44
2793 7262 6.173427 ACAGCTCCACCAAAATTACAATTT 57.827 33.333 0.00 0.00 40.15 1.82
2932 7414 3.748568 ACAAGTCTTTCCGCTTCATTCTC 59.251 43.478 0.00 0.00 0.00 2.87
2936 7418 2.012673 CTTTCCGCTTCATTCTCCCTG 58.987 52.381 0.00 0.00 0.00 4.45
2956 7438 1.339055 GGATGTACACTGCCTGCAGAA 60.339 52.381 24.88 7.68 46.30 3.02
2957 7439 2.426522 GATGTACACTGCCTGCAGAAA 58.573 47.619 24.88 7.34 46.30 2.52
2987 7488 2.102578 AGTGTTTGGTGCAAAGCTCTT 58.897 42.857 0.00 0.00 33.82 2.85
3061 7562 5.768164 GGGAAACAGTGATAAAAGGAACAGA 59.232 40.000 0.00 0.00 0.00 3.41
3079 7580 1.338973 AGAGCGACAAGTGAAACGGTA 59.661 47.619 0.00 0.00 45.86 4.02
3118 7619 3.609175 CGGTTCATTCAACAACGAGCATT 60.609 43.478 0.00 0.00 36.61 3.56
3191 7700 0.534412 CGAACACTCCAGCTCCTCAT 59.466 55.000 0.00 0.00 0.00 2.90
3192 7701 1.470632 CGAACACTCCAGCTCCTCATC 60.471 57.143 0.00 0.00 0.00 2.92
3211 7720 0.737367 CGACGATTTGCAGCTCCTCA 60.737 55.000 0.00 0.00 0.00 3.86
3216 7725 1.596727 GATTTGCAGCTCCTCATCGAC 59.403 52.381 0.00 0.00 0.00 4.20
3225 7734 1.081774 CCTCATCGACGATCTCGCC 60.082 63.158 7.54 0.00 42.62 5.54
3246 7755 2.694760 AACTCGGGGTAGCGACGAC 61.695 63.158 0.00 0.00 32.66 4.34
3247 7756 3.129502 CTCGGGGTAGCGACGACA 61.130 66.667 0.00 0.00 32.66 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 4.016444 ACATAGTAATGGCCAGGTGTTTG 58.984 43.478 13.05 7.74 37.43 2.93
163 165 4.038642 GGCATGTTCTTGTAGGAAACCAAA 59.961 41.667 0.00 0.00 0.00 3.28
187 190 6.861065 AGGTTATTCAGTATATGGTTTGCG 57.139 37.500 0.00 0.00 0.00 4.85
226 230 8.951787 TCTTAGAAAAGTGTGTGCTAAAGTAA 57.048 30.769 0.00 0.00 34.13 2.24
377 381 1.329906 CTTATGCAAGAAGCTGCTCCG 59.670 52.381 1.00 0.00 45.94 4.63
391 395 4.866486 CCTTTCTTCATGTTTGCCTTATGC 59.134 41.667 0.00 0.00 41.77 3.14
523 537 9.662545 GATGTAAAAGTCTCGATAGGTACTTAC 57.337 37.037 0.00 0.00 39.45 2.34
742 760 4.697756 TTGCGAGGGAACGGGCTG 62.698 66.667 0.00 0.00 34.96 4.85
743 761 2.969300 TTTTTGCGAGGGAACGGGCT 62.969 55.000 0.00 0.00 34.96 5.19
744 762 2.557372 TTTTTGCGAGGGAACGGGC 61.557 57.895 0.00 0.00 0.00 6.13
745 763 3.752704 TTTTTGCGAGGGAACGGG 58.247 55.556 0.00 0.00 0.00 5.28
769 787 4.760047 CACGGAGGAACGGGCTGG 62.760 72.222 0.00 0.00 38.39 4.85
770 788 4.003788 ACACGGAGGAACGGGCTG 62.004 66.667 0.00 0.00 41.99 4.85
812 5184 4.261572 GCAGCATTACAGACCACTCAAAAA 60.262 41.667 0.00 0.00 0.00 1.94
813 5185 3.253188 GCAGCATTACAGACCACTCAAAA 59.747 43.478 0.00 0.00 0.00 2.44
814 5186 2.813754 GCAGCATTACAGACCACTCAAA 59.186 45.455 0.00 0.00 0.00 2.69
815 5187 2.426522 GCAGCATTACAGACCACTCAA 58.573 47.619 0.00 0.00 0.00 3.02
816 5188 1.672737 CGCAGCATTACAGACCACTCA 60.673 52.381 0.00 0.00 0.00 3.41
817 5189 1.002366 CGCAGCATTACAGACCACTC 58.998 55.000 0.00 0.00 0.00 3.51
818 5190 0.321671 ACGCAGCATTACAGACCACT 59.678 50.000 0.00 0.00 0.00 4.00
819 5191 2.004583 TACGCAGCATTACAGACCAC 57.995 50.000 0.00 0.00 0.00 4.16
820 5192 2.093711 ACATACGCAGCATTACAGACCA 60.094 45.455 0.00 0.00 0.00 4.02
821 5193 2.285220 CACATACGCAGCATTACAGACC 59.715 50.000 0.00 0.00 0.00 3.85
822 5194 3.000322 GTCACATACGCAGCATTACAGAC 60.000 47.826 0.00 0.00 0.00 3.51
823 5195 3.186909 GTCACATACGCAGCATTACAGA 58.813 45.455 0.00 0.00 0.00 3.41
824 5196 2.285220 GGTCACATACGCAGCATTACAG 59.715 50.000 0.00 0.00 0.00 2.74
825 5197 2.093711 AGGTCACATACGCAGCATTACA 60.094 45.455 0.00 0.00 0.00 2.41
826 5198 2.550978 AGGTCACATACGCAGCATTAC 58.449 47.619 0.00 0.00 0.00 1.89
827 5199 2.979814 AGGTCACATACGCAGCATTA 57.020 45.000 0.00 0.00 0.00 1.90
828 5200 2.009774 GAAGGTCACATACGCAGCATT 58.990 47.619 0.00 0.00 0.00 3.56
829 5201 1.066215 TGAAGGTCACATACGCAGCAT 60.066 47.619 0.00 0.00 0.00 3.79
830 5202 0.320050 TGAAGGTCACATACGCAGCA 59.680 50.000 0.00 0.00 0.00 4.41
831 5203 1.128692 GTTGAAGGTCACATACGCAGC 59.871 52.381 0.00 0.00 0.00 5.25
832 5204 2.412870 TGTTGAAGGTCACATACGCAG 58.587 47.619 0.00 0.00 0.00 5.18
833 5205 2.412870 CTGTTGAAGGTCACATACGCA 58.587 47.619 0.00 0.00 0.00 5.24
834 5206 1.732259 CCTGTTGAAGGTCACATACGC 59.268 52.381 0.00 0.00 41.74 4.42
852 5224 5.807605 GGCTTTGAGCAGCTAACTAGCCT 62.808 52.174 19.30 0.00 44.75 4.58
853 5225 3.574113 GGCTTTGAGCAGCTAACTAGCC 61.574 54.545 14.04 14.04 44.75 3.93
854 5226 1.668237 GGCTTTGAGCAGCTAACTAGC 59.332 52.381 0.00 0.00 44.75 3.42
855 5227 2.284190 GGGCTTTGAGCAGCTAACTAG 58.716 52.381 0.00 0.00 44.75 2.57
856 5228 1.628340 TGGGCTTTGAGCAGCTAACTA 59.372 47.619 0.00 0.00 44.75 2.24
857 5229 0.401738 TGGGCTTTGAGCAGCTAACT 59.598 50.000 0.00 0.00 44.75 2.24
858 5230 0.807496 CTGGGCTTTGAGCAGCTAAC 59.193 55.000 0.00 0.00 44.75 2.34
859 5231 0.401738 ACTGGGCTTTGAGCAGCTAA 59.598 50.000 0.00 0.00 44.75 3.09
860 5232 0.036010 GACTGGGCTTTGAGCAGCTA 60.036 55.000 0.00 0.00 44.75 3.32
893 5265 3.771577 TGAAAACCTCCTGAACTCCTC 57.228 47.619 0.00 0.00 0.00 3.71
965 5377 6.839820 ATCGAATACGTTTATGTTTCCTCC 57.160 37.500 0.00 0.00 40.69 4.30
1051 5470 0.940126 GCATGCTTGGATGGAGTACG 59.060 55.000 11.37 0.00 0.00 3.67
1069 5493 3.454371 ACATACAACGTAGGGAGATGC 57.546 47.619 0.00 0.00 0.00 3.91
1078 5502 9.627123 AATACCTAGTTACCTACATACAACGTA 57.373 33.333 0.00 0.00 0.00 3.57
1091 5515 5.269313 CGTCTCGTTGAATACCTAGTTACC 58.731 45.833 0.00 0.00 0.00 2.85
1092 5516 5.269313 CCGTCTCGTTGAATACCTAGTTAC 58.731 45.833 0.00 0.00 0.00 2.50
1093 5517 4.201950 GCCGTCTCGTTGAATACCTAGTTA 60.202 45.833 0.00 0.00 0.00 2.24
1094 5518 3.428589 GCCGTCTCGTTGAATACCTAGTT 60.429 47.826 0.00 0.00 0.00 2.24
1095 5519 2.098770 GCCGTCTCGTTGAATACCTAGT 59.901 50.000 0.00 0.00 0.00 2.57
1096 5520 2.543238 GGCCGTCTCGTTGAATACCTAG 60.543 54.545 0.00 0.00 0.00 3.02
1097 5521 1.406539 GGCCGTCTCGTTGAATACCTA 59.593 52.381 0.00 0.00 0.00 3.08
1098 5522 0.175073 GGCCGTCTCGTTGAATACCT 59.825 55.000 0.00 0.00 0.00 3.08
1099 5523 0.175073 AGGCCGTCTCGTTGAATACC 59.825 55.000 0.00 0.00 0.00 2.73
1496 5923 1.880819 TTCAGGACGTAGAACCCGCC 61.881 60.000 0.00 0.00 0.00 6.13
1553 5980 5.171476 TGTCGAATGAAGGATCTTGTCTTC 58.829 41.667 0.00 0.00 39.66 2.87
1614 6043 4.988598 ACAGCCGCACGACCTTGG 62.989 66.667 0.00 0.00 0.00 3.61
1647 6076 0.038166 GAATGCTTCCCAGGGTGTCA 59.962 55.000 5.01 1.98 0.00 3.58
1655 6084 1.383799 CCCTGGTGAATGCTTCCCA 59.616 57.895 0.00 0.00 0.00 4.37
1715 6144 0.603569 ACGCCTTCGACAGAGATTGT 59.396 50.000 0.00 0.00 44.55 2.71
1717 6146 0.737715 GCACGCCTTCGACAGAGATT 60.738 55.000 0.00 0.00 39.41 2.40
1738 6167 4.090057 GCCTCCGCGAACTTGCAC 62.090 66.667 8.23 0.00 34.15 4.57
1770 6203 1.009675 GCCAGTTTGTCGCACACAG 60.010 57.895 0.00 0.00 35.97 3.66
1778 6211 1.381165 AACACCGGTGCCAGTTTGTC 61.381 55.000 34.26 0.00 0.00 3.18
1809 6242 2.068915 TGGATGAGCCAGTGCAGAA 58.931 52.632 0.00 0.00 43.33 3.02
1885 6318 1.581954 CCAGCTGAACGTCTCGTCT 59.418 57.895 17.39 0.00 39.99 4.18
2029 6462 2.711009 CCAGCCACCATTATCTTCCCTA 59.289 50.000 0.00 0.00 0.00 3.53
2046 6487 2.894387 GATGCTCCAGCGACCAGC 60.894 66.667 0.00 0.00 45.83 4.85
2065 6506 0.319211 CAAGCCGTACCAAGTCGACA 60.319 55.000 19.50 0.00 0.00 4.35
2254 6695 1.221466 TTCTTGCAACAGGTCGCTCG 61.221 55.000 0.00 0.00 0.00 5.03
2432 6888 2.603953 GGAGTTAAGACGTACAGCACC 58.396 52.381 0.00 0.00 0.00 5.01
2438 6894 2.614779 GCAAGGGGAGTTAAGACGTAC 58.385 52.381 0.00 0.00 0.00 3.67
2439 6895 1.551883 GGCAAGGGGAGTTAAGACGTA 59.448 52.381 0.00 0.00 0.00 3.57
2440 6896 0.323957 GGCAAGGGGAGTTAAGACGT 59.676 55.000 0.00 0.00 0.00 4.34
2441 6897 0.613777 AGGCAAGGGGAGTTAAGACG 59.386 55.000 0.00 0.00 0.00 4.18
2517 6984 3.744426 AGCTATGACACCGTACAACAAAC 59.256 43.478 0.00 0.00 0.00 2.93
2578 7047 3.420893 TCGGGAAACTCAGAAATTGCAT 58.579 40.909 0.00 0.00 0.00 3.96
2653 7122 0.457851 CCCTGAGCCGAGAACTACAG 59.542 60.000 0.00 0.00 0.00 2.74
2683 7152 1.128200 GGGTTTTGCCTGAAGGGTTT 58.872 50.000 0.00 0.00 37.43 3.27
2769 7238 5.806654 ATTGTAATTTTGGTGGAGCTGTT 57.193 34.783 0.00 0.00 0.00 3.16
2784 7253 9.778741 TGAAGACAGTTCACTCTAAATTGTAAT 57.221 29.630 0.00 0.00 28.14 1.89
2807 7276 1.243902 GGAATGTTCGGGCAAGTGAA 58.756 50.000 0.00 0.00 0.00 3.18
2932 7414 0.107508 CAGGCAGTGTACATCCAGGG 60.108 60.000 0.00 0.00 0.00 4.45
2936 7418 0.250234 TCTGCAGGCAGTGTACATCC 59.750 55.000 19.75 1.03 43.96 3.51
2956 7438 6.031751 TGCACCAAACACTTTAAAGTTCTT 57.968 33.333 18.25 11.27 37.08 2.52
2957 7439 5.652994 TGCACCAAACACTTTAAAGTTCT 57.347 34.783 18.25 5.68 37.08 3.01
2987 7488 6.241882 TGTAATCGGGATGGAATTTCTGTA 57.758 37.500 0.00 0.00 0.00 2.74
3028 7529 1.021390 CACTGTTTCCCGCTGGCTAG 61.021 60.000 0.00 0.00 0.00 3.42
3037 7538 5.768164 TCTGTTCCTTTTATCACTGTTTCCC 59.232 40.000 0.00 0.00 0.00 3.97
3061 7562 1.202440 TGTACCGTTTCACTTGTCGCT 60.202 47.619 0.00 0.00 0.00 4.93
3079 7580 8.611654 AATGAACCGTTATGTACTTTTACTGT 57.388 30.769 0.00 0.00 0.00 3.55
3118 7619 0.610174 AGAAGATCCAACAGCTCGCA 59.390 50.000 0.00 0.00 0.00 5.10
3191 7700 0.458543 GAGGAGCTGCAAATCGTCGA 60.459 55.000 8.35 0.00 0.00 4.20
3192 7701 0.737367 TGAGGAGCTGCAAATCGTCG 60.737 55.000 8.35 0.00 33.98 5.12
3216 7725 3.315521 CGAGTTGCGGCGAGATCG 61.316 66.667 12.98 10.53 43.27 3.69
3242 7751 1.468224 CGAGCAGCTGTAGATTGTCGT 60.468 52.381 16.64 0.00 0.00 4.34
3246 7755 1.195347 CGACGAGCAGCTGTAGATTG 58.805 55.000 16.64 5.89 0.00 2.67
3247 7756 1.095600 TCGACGAGCAGCTGTAGATT 58.904 50.000 16.64 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.