Multiple sequence alignment - TraesCS5B01G427200

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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 TraesCS5B01G427200 chr5B 100.000 3212 0 0 1 3212 603459322 603456111 0.000000e+00 5932.0
1 TraesCS5B01G427200 chr5B 87.452 781 90 6 1 778 254871490 254872265 0.000000e+00 893.0
2 TraesCS5B01G427200 chr5B 94.495 109 6 0 2679 2787 306435391 306435283 5.510000e-38 169.0
3 TraesCS5B01G427200 chr5D 96.929 1791 49 2 899 2689 489313232 489311448 0.000000e+00 2998.0
4 TraesCS5B01G427200 chr5D 96.288 431 15 1 2781 3211 489311451 489311022 0.000000e+00 706.0
5 TraesCS5B01G427200 chr5D 93.590 78 5 0 836 913 489316289 489316212 2.020000e-22 117.0
6 TraesCS5B01G427200 chr5D 97.674 43 1 0 789 831 489316354 489316312 1.240000e-09 75.0
7 TraesCS5B01G427200 chr5A 95.523 1854 65 5 836 2689 610465247 610463412 0.000000e+00 2948.0
8 TraesCS5B01G427200 chr5A 96.074 433 15 2 2781 3211 610463415 610462983 0.000000e+00 704.0
9 TraesCS5B01G427200 chr7B 92.021 777 59 3 1 775 297684183 297684958 0.000000e+00 1088.0
10 TraesCS5B01G427200 chr2D 89.704 777 72 6 1 775 244599400 244600170 0.000000e+00 985.0
11 TraesCS5B01G427200 chr2D 89.433 776 74 6 1 775 244595107 244595875 0.000000e+00 972.0
12 TraesCS5B01G427200 chr3D 89.474 779 72 8 1 776 19194581 19195352 0.000000e+00 976.0
13 TraesCS5B01G427200 chr3D 87.372 784 87 9 1 778 528338990 528338213 0.000000e+00 889.0
14 TraesCS5B01G427200 chr6D 88.846 780 74 8 1 776 437595992 437596762 0.000000e+00 946.0
15 TraesCS5B01G427200 chr6D 88.703 779 76 7 1 775 437556339 437557109 0.000000e+00 941.0
16 TraesCS5B01G427200 chr1B 88.342 772 74 8 10 775 359009270 359008509 0.000000e+00 913.0
17 TraesCS5B01G427200 chr1B 94.643 112 3 2 2684 2792 328139786 328139675 1.530000e-38 171.0
18 TraesCS5B01G427200 chr1B 92.308 117 7 2 2681 2795 429610630 429610746 7.130000e-37 165.0
19 TraesCS5B01G427200 chr1B 95.556 45 2 0 3001 3045 410814066 410814022 4.440000e-09 73.1
20 TraesCS5B01G427200 chr2B 92.857 126 8 1 2684 2809 418953564 418953688 7.080000e-42 182.0
21 TraesCS5B01G427200 chr2B 94.595 111 5 1 2677 2787 397939364 397939473 1.530000e-38 171.0
22 TraesCS5B01G427200 chr2B 93.750 112 6 1 2676 2787 425527645 425527755 1.980000e-37 167.0
23 TraesCS5B01G427200 chr6B 97.030 101 3 0 2686 2786 517835972 517836072 1.530000e-38 171.0
24 TraesCS5B01G427200 chr4B 94.495 109 6 0 2684 2792 186741667 186741775 5.510000e-38 169.0
25 TraesCS5B01G427200 chr1D 92.241 116 9 0 2684 2799 473539224 473539109 7.130000e-37 165.0
26 TraesCS5B01G427200 chr2A 78.696 230 33 13 2994 3211 171956037 171955812 4.320000e-29 139.0


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 TraesCS5B01G427200 chr5B 603456111 603459322 3211 True 5932.0 5932 100.00000 1 3212 1 chr5B.!!$R2 3211
1 TraesCS5B01G427200 chr5B 254871490 254872265 775 False 893.0 893 87.45200 1 778 1 chr5B.!!$F1 777
2 TraesCS5B01G427200 chr5D 489311022 489316354 5332 True 974.0 2998 96.12025 789 3211 4 chr5D.!!$R1 2422
3 TraesCS5B01G427200 chr5A 610462983 610465247 2264 True 1826.0 2948 95.79850 836 3211 2 chr5A.!!$R1 2375
4 TraesCS5B01G427200 chr7B 297684183 297684958 775 False 1088.0 1088 92.02100 1 775 1 chr7B.!!$F1 774
5 TraesCS5B01G427200 chr2D 244595107 244600170 5063 False 978.5 985 89.56850 1 775 2 chr2D.!!$F1 774
6 TraesCS5B01G427200 chr3D 19194581 19195352 771 False 976.0 976 89.47400 1 776 1 chr3D.!!$F1 775
7 TraesCS5B01G427200 chr3D 528338213 528338990 777 True 889.0 889 87.37200 1 778 1 chr3D.!!$R1 777
8 TraesCS5B01G427200 chr6D 437595992 437596762 770 False 946.0 946 88.84600 1 776 1 chr6D.!!$F2 775
9 TraesCS5B01G427200 chr6D 437556339 437557109 770 False 941.0 941 88.70300 1 775 1 chr6D.!!$F1 774
10 TraesCS5B01G427200 chr1B 359008509 359009270 761 True 913.0 913 88.34200 10 775 1 chr1B.!!$R2 765

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
831 5136 0.035534 CCACCAATCCACCACGATCA 60.036 55.0 0.00 0.0 0.00 2.92 F
1590 8907 0.533755 CCGAGGATGAGAACCATGGC 60.534 60.0 13.04 0.0 35.17 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 9381 0.108186 CATACTTGCTCCGCACCTCA 60.108 55.0 0.0 0.0 38.71 3.86 R
2933 10251 0.396974 AACAACACTGGGCCACACAT 60.397 50.0 0.0 0.0 0.00 3.21 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
117 119 3.049674 CGCGCCCACAAGACATGT 61.050 61.111 0.00 0.00 45.34 3.21
174 176 2.034999 AGCGATTCGGCCCCAAAA 59.965 55.556 8.34 0.00 0.00 2.44
223 225 6.961359 ACATGAAAATTATTCGTCTCGTCA 57.039 33.333 0.00 0.00 0.00 4.35
384 387 2.296190 GGACGTGAATCCAAGCCTTTTT 59.704 45.455 0.00 0.00 38.77 1.94
394 397 0.249447 AAGCCTTTTTCTTGCACGGC 60.249 50.000 0.00 0.00 37.80 5.68
424 430 3.768215 GCCGCCTCTTATATACCTAAGGT 59.232 47.826 0.00 0.00 40.16 3.50
446 455 1.959985 TGACGGCCAATTGAACAACAT 59.040 42.857 7.12 0.00 0.00 2.71
448 457 3.761218 TGACGGCCAATTGAACAACATAT 59.239 39.130 7.12 0.00 0.00 1.78
525 534 4.948621 CCCTAGTTCTTCTTCTTCCTCGTA 59.051 45.833 0.00 0.00 0.00 3.43
599 609 1.112315 CAGGTCGATCTAGGGCAGCT 61.112 60.000 0.00 0.00 0.00 4.24
631 641 3.003763 GCCCTGACGAGGTCCCTT 61.004 66.667 0.00 0.00 37.73 3.95
705 5010 4.796231 CGCTTCCGGACGGGTCTG 62.796 72.222 15.92 0.54 37.00 3.51
780 5085 3.355816 TCGTGTGCGAACAGAAAGT 57.644 47.368 0.00 0.00 44.92 2.66
781 5086 1.205657 TCGTGTGCGAACAGAAAGTC 58.794 50.000 0.00 0.00 44.92 3.01
782 5087 0.927537 CGTGTGCGAACAGAAAGTCA 59.072 50.000 0.00 0.00 41.33 3.41
783 5088 1.332028 CGTGTGCGAACAGAAAGTCAC 60.332 52.381 0.00 0.00 41.33 3.67
784 5089 1.933853 GTGTGCGAACAGAAAGTCACT 59.066 47.619 0.00 0.00 0.00 3.41
785 5090 3.120792 GTGTGCGAACAGAAAGTCACTA 58.879 45.455 0.00 0.00 0.00 2.74
786 5091 3.554324 GTGTGCGAACAGAAAGTCACTAA 59.446 43.478 0.00 0.00 0.00 2.24
787 5092 4.211374 GTGTGCGAACAGAAAGTCACTAAT 59.789 41.667 0.00 0.00 0.00 1.73
826 5131 2.679996 GGGCCACCAATCCACCAC 60.680 66.667 4.39 0.00 36.50 4.16
831 5136 0.035534 CCACCAATCCACCACGATCA 60.036 55.000 0.00 0.00 0.00 2.92
848 5171 4.988716 ACAGCCCGACTCCGACCA 62.989 66.667 0.00 0.00 38.22 4.02
881 5204 4.856607 GAGAAGCTCCGACCGCCG 62.857 72.222 0.00 0.00 38.18 6.46
907 8224 1.680207 GGCGTCCGTTCTACTATCCTT 59.320 52.381 0.00 0.00 0.00 3.36
926 8243 1.219393 CTTCTTCCACCTCCGCCTC 59.781 63.158 0.00 0.00 0.00 4.70
929 8246 4.332543 TTCCACCTCCGCCTCCCT 62.333 66.667 0.00 0.00 0.00 4.20
1590 8907 0.533755 CCGAGGATGAGAACCATGGC 60.534 60.000 13.04 0.00 35.17 4.40
1791 9108 6.067961 TGCCTTATATCTCTCCCTATGAGGAT 60.068 42.308 4.97 0.00 41.76 3.24
1803 9120 4.518211 CCCTATGAGGATTTCAGCAACATC 59.482 45.833 0.00 0.00 39.68 3.06
1908 9225 1.805945 GCGACGGTTACTCTGCCTG 60.806 63.158 0.00 0.00 0.00 4.85
1941 9258 2.508526 GGGCTGTCACAGAAGTTTCAT 58.491 47.619 9.70 0.00 32.44 2.57
1962 9279 2.904866 GTGTTTGAGCGGCACCCA 60.905 61.111 1.45 0.00 0.00 4.51
2055 9372 3.693085 GACACACATCAATTGAGGAGCAT 59.307 43.478 25.68 10.05 0.00 3.79
2263 9581 0.033601 AGGAAATGGGCAATACGGCA 60.034 50.000 0.00 0.00 43.60 5.69
2343 9661 4.039004 TGCATGCAAATAAAGGAGTTGTGT 59.961 37.500 20.30 0.00 35.52 3.72
2524 9842 6.511121 GCGAATGACTTTTACTTGTTCACTGA 60.511 38.462 0.00 0.00 0.00 3.41
2577 9895 7.667219 TCTTGAACATCTTTTCTTCCTGCTTAT 59.333 33.333 0.00 0.00 0.00 1.73
2645 9963 4.403113 TGGGAAACTTTTTAGGAAAACGCT 59.597 37.500 0.00 0.00 31.72 5.07
2686 10004 8.522830 CAAATAACAGGCAGGATCTTTTCTTAA 58.477 33.333 0.00 0.00 0.00 1.85
2687 10005 8.829373 AATAACAGGCAGGATCTTTTCTTAAT 57.171 30.769 0.00 0.00 0.00 1.40
2688 10006 9.920946 AATAACAGGCAGGATCTTTTCTTAATA 57.079 29.630 0.00 0.00 0.00 0.98
2689 10007 7.631717 AACAGGCAGGATCTTTTCTTAATAC 57.368 36.000 0.00 0.00 0.00 1.89
2690 10008 6.963322 ACAGGCAGGATCTTTTCTTAATACT 58.037 36.000 0.00 0.00 0.00 2.12
2691 10009 7.051000 ACAGGCAGGATCTTTTCTTAATACTC 58.949 38.462 0.00 0.00 0.00 2.59
2692 10010 6.484977 CAGGCAGGATCTTTTCTTAATACTCC 59.515 42.308 0.00 0.00 0.00 3.85
2693 10011 5.765677 GGCAGGATCTTTTCTTAATACTCCC 59.234 44.000 0.00 0.00 0.00 4.30
2694 10012 6.409810 GGCAGGATCTTTTCTTAATACTCCCT 60.410 42.308 0.00 0.00 0.00 4.20
2695 10013 6.708502 GCAGGATCTTTTCTTAATACTCCCTC 59.291 42.308 0.00 0.00 0.00 4.30
2696 10014 7.220740 CAGGATCTTTTCTTAATACTCCCTCC 58.779 42.308 0.00 0.00 0.00 4.30
2697 10015 6.042208 AGGATCTTTTCTTAATACTCCCTCCG 59.958 42.308 0.00 0.00 0.00 4.63
2698 10016 6.183360 GGATCTTTTCTTAATACTCCCTCCGT 60.183 42.308 0.00 0.00 0.00 4.69
2699 10017 6.218108 TCTTTTCTTAATACTCCCTCCGTC 57.782 41.667 0.00 0.00 0.00 4.79
2700 10018 5.128335 TCTTTTCTTAATACTCCCTCCGTCC 59.872 44.000 0.00 0.00 0.00 4.79
2701 10019 2.954792 TCTTAATACTCCCTCCGTCCC 58.045 52.381 0.00 0.00 0.00 4.46
2702 10020 2.245546 TCTTAATACTCCCTCCGTCCCA 59.754 50.000 0.00 0.00 0.00 4.37
2703 10021 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2704 10022 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2705 10023 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2706 10024 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2707 10025 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2708 10026 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2709 10027 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2710 10028 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2711 10029 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2712 10030 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2713 10031 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2714 10032 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2715 10033 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2716 10034 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
2717 10035 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
2718 10036 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
2719 10037 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
2720 10038 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
2721 10039 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2722 10040 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
2723 10041 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2724 10042 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2725 10043 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2726 10044 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2727 10045 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
2728 10046 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2729 10047 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
2730 10048 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
2731 10049 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
2732 10050 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
2733 10051 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
2734 10052 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
2735 10053 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
2736 10054 9.502091 TGTCTTGAGCTTAGTACAAATTTGTAT 57.498 29.630 28.69 20.33 44.59 2.29
2743 10061 9.892130 AGCTTAGTACAAATTTGTATTAGAGCT 57.108 29.630 31.75 31.75 44.59 4.09
2748 10066 9.819267 AGTACAAATTTGTATTAGAGCTAGTCC 57.181 33.333 28.69 14.08 44.59 3.85
2749 10067 9.595823 GTACAAATTTGTATTAGAGCTAGTCCA 57.404 33.333 28.69 4.97 44.59 4.02
2751 10069 9.515226 ACAAATTTGTATTAGAGCTAGTCCAAA 57.485 29.630 22.10 0.00 40.16 3.28
2752 10070 9.994432 CAAATTTGTATTAGAGCTAGTCCAAAG 57.006 33.333 10.15 0.00 0.00 2.77
2753 10071 9.740710 AAATTTGTATTAGAGCTAGTCCAAAGT 57.259 29.630 0.00 0.00 0.00 2.66
2754 10072 9.740710 AATTTGTATTAGAGCTAGTCCAAAGTT 57.259 29.630 0.00 0.00 0.00 2.66
2755 10073 8.547967 TTTGTATTAGAGCTAGTCCAAAGTTG 57.452 34.615 0.00 0.00 0.00 3.16
2756 10074 7.476540 TGTATTAGAGCTAGTCCAAAGTTGA 57.523 36.000 0.00 0.00 0.00 3.18
2757 10075 7.548097 TGTATTAGAGCTAGTCCAAAGTTGAG 58.452 38.462 0.00 0.00 0.00 3.02
2758 10076 6.859112 ATTAGAGCTAGTCCAAAGTTGAGA 57.141 37.500 0.00 0.00 0.00 3.27
2759 10077 4.529109 AGAGCTAGTCCAAAGTTGAGAC 57.471 45.455 0.00 0.00 0.00 3.36
2760 10078 3.898123 AGAGCTAGTCCAAAGTTGAGACA 59.102 43.478 12.28 0.00 33.58 3.41
2761 10079 3.991121 GAGCTAGTCCAAAGTTGAGACAC 59.009 47.826 12.28 4.90 33.58 3.67
2762 10080 3.643792 AGCTAGTCCAAAGTTGAGACACT 59.356 43.478 12.28 6.38 33.58 3.55
2763 10081 4.101741 AGCTAGTCCAAAGTTGAGACACTT 59.898 41.667 12.28 0.00 38.74 3.16
2764 10082 5.304614 AGCTAGTCCAAAGTTGAGACACTTA 59.695 40.000 12.28 0.95 35.87 2.24
2765 10083 6.014156 AGCTAGTCCAAAGTTGAGACACTTAT 60.014 38.462 12.28 0.00 35.87 1.73
2766 10084 6.651225 GCTAGTCCAAAGTTGAGACACTTATT 59.349 38.462 12.28 0.00 35.87 1.40
2767 10085 7.173390 GCTAGTCCAAAGTTGAGACACTTATTT 59.827 37.037 12.28 0.00 35.87 1.40
2768 10086 7.881775 AGTCCAAAGTTGAGACACTTATTTT 57.118 32.000 12.28 0.00 35.87 1.82
2769 10087 7.707104 AGTCCAAAGTTGAGACACTTATTTTG 58.293 34.615 12.28 0.00 35.87 2.44
2770 10088 6.918022 GTCCAAAGTTGAGACACTTATTTTGG 59.082 38.462 6.37 6.37 42.76 3.28
2771 10089 6.040391 TCCAAAGTTGAGACACTTATTTTGGG 59.960 38.462 11.43 0.00 42.07 4.12
2772 10090 6.040391 CCAAAGTTGAGACACTTATTTTGGGA 59.960 38.462 5.07 0.00 39.54 4.37
2773 10091 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2774 10092 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2775 10093 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2776 10094 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2777 10095 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2778 10096 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2779 10097 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2780 10098 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2796 10114 7.094762 GGACGGAGGGAATATTAATTAAGCTTG 60.095 40.741 9.86 0.00 0.00 4.01
2801 10119 9.131791 GAGGGAATATTAATTAAGCTTGAACCA 57.868 33.333 9.86 0.00 0.00 3.67
2887 10205 9.800433 TGTTGGTATGTGCAGAATAAATAAATG 57.200 29.630 0.00 0.00 0.00 2.32
2958 10276 0.534873 GGCCCAGTGTTGTTGTTTGT 59.465 50.000 0.00 0.00 0.00 2.83
3174 10494 8.508883 TTTACCTGCACAAAGTTAAAGACTAA 57.491 30.769 0.00 0.00 37.72 2.24
3194 10514 8.142551 AGACTAAGATGACAGAAACGTTTAACT 58.857 33.333 14.65 4.87 0.00 2.24
3211 10531 9.389570 ACGTTTAACTAACTCATGCAATAAAAC 57.610 29.630 0.00 0.00 34.46 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.205719 CCTGAATTGAGATGAGTTGTATATCAG 57.794 37.037 0.00 0.00 28.73 2.90
117 119 1.220749 GGCGCTACCCATCAGACAA 59.779 57.895 7.64 0.00 0.00 3.18
211 213 2.144482 ACCGTTTTGACGAGACGAAT 57.856 45.000 7.32 0.00 38.99 3.34
223 225 8.178964 GCTTCCAAAAGAAAATTTAACCGTTTT 58.821 29.630 0.00 0.00 34.14 2.43
394 397 0.179000 ATAAGAGGCGGCTGGACTTG 59.821 55.000 19.63 0.00 29.96 3.16
424 430 1.066303 GTTGTTCAATTGGCCGTCACA 59.934 47.619 5.42 0.00 0.00 3.58
569 579 3.550431 CGACCTGATCGCCCCCAT 61.550 66.667 0.00 0.00 45.52 4.00
705 5010 3.832171 CGCAGCTCACGTCGAAGC 61.832 66.667 13.93 13.93 0.00 3.86
737 5042 1.108727 TCACCGTGTACCTCCAACGT 61.109 55.000 0.00 0.00 35.59 3.99
778 5083 5.474578 TCACTTGCTGAAGATTAGTGACT 57.525 39.130 0.00 0.00 40.01 3.41
780 5085 5.213891 TGTCACTTGCTGAAGATTAGTGA 57.786 39.130 0.00 0.00 41.94 3.41
781 5086 5.929697 TTGTCACTTGCTGAAGATTAGTG 57.070 39.130 0.00 0.00 38.00 2.74
782 5087 5.106396 GCATTGTCACTTGCTGAAGATTAGT 60.106 40.000 0.00 0.00 35.95 2.24
783 5088 5.123502 AGCATTGTCACTTGCTGAAGATTAG 59.876 40.000 8.34 0.00 46.96 1.73
784 5089 5.005740 AGCATTGTCACTTGCTGAAGATTA 58.994 37.500 8.34 0.00 46.96 1.75
785 5090 3.825014 AGCATTGTCACTTGCTGAAGATT 59.175 39.130 8.34 0.00 46.96 2.40
786 5091 3.418995 AGCATTGTCACTTGCTGAAGAT 58.581 40.909 8.34 0.00 46.96 2.40
787 5092 2.854963 AGCATTGTCACTTGCTGAAGA 58.145 42.857 8.34 0.00 46.96 2.87
826 5131 2.105128 GGAGTCGGGCTGTGATCG 59.895 66.667 0.00 0.00 0.00 3.69
831 5136 4.988716 TGGTCGGAGTCGGGCTGT 62.989 66.667 2.08 0.00 36.95 4.40
903 5226 1.267121 CGGAGGTGGAAGAAGAAGGA 58.733 55.000 0.00 0.00 0.00 3.36
907 8224 1.229209 AGGCGGAGGTGGAAGAAGA 60.229 57.895 0.00 0.00 0.00 2.87
926 8243 2.982130 CGGTGAAGAGGTGGAGGG 59.018 66.667 0.00 0.00 0.00 4.30
929 8246 3.691342 CGGCGGTGAAGAGGTGGA 61.691 66.667 0.00 0.00 0.00 4.02
1508 8825 0.107410 CCCAATGTCGAAATCCGGGA 60.107 55.000 15.27 0.00 39.14 5.14
1611 8928 4.498682 GGCATTTCTTGATCTTTCCCATCG 60.499 45.833 0.00 0.00 0.00 3.84
1791 9108 1.462616 CCCGATGGATGTTGCTGAAA 58.537 50.000 0.00 0.00 0.00 2.69
1851 9168 2.033407 CACAAACAGACTGAACAGCTCG 60.033 50.000 10.08 0.00 0.00 5.03
1908 9225 2.930562 AGCCCCAGGTGTGTCCTC 60.931 66.667 0.00 0.00 46.24 3.71
1941 9258 1.891919 GTGCCGCTCAAACACCAGA 60.892 57.895 0.00 0.00 0.00 3.86
2055 9372 2.046023 CGCACCTCAAGCATGGGA 60.046 61.111 0.00 0.00 0.00 4.37
2064 9381 0.108186 CATACTTGCTCCGCACCTCA 60.108 55.000 0.00 0.00 38.71 3.86
2139 9456 2.467880 TCCTCAGGATCCAACTGTACC 58.532 52.381 15.82 0.00 37.25 3.34
2239 9557 4.558697 GCCGTATTGCCCATTTCCTTATTC 60.559 45.833 0.00 0.00 0.00 1.75
2360 9678 4.621460 CGGTAAATCATAGATACTGCACCG 59.379 45.833 0.00 0.00 39.18 4.94
2524 9842 4.099881 ACATTGGAAAGTCACAACAGCATT 59.900 37.500 0.00 0.00 0.00 3.56
2577 9895 9.005777 ACACTTTCTGTTGTTAGTTTTCACTTA 57.994 29.630 0.00 0.00 34.06 2.24
2645 9963 4.764308 TGTTATTTGCCAGTAGATGTTGCA 59.236 37.500 0.00 0.00 0.00 4.08
2673 9991 6.183360 ACGGAGGGAGTATTAAGAAAAGATCC 60.183 42.308 0.00 0.00 0.00 3.36
2686 10004 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2687 10005 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2688 10006 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2689 10007 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2690 10008 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2691 10009 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2692 10010 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2693 10011 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2694 10012 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
2695 10013 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
2696 10014 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
2697 10015 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
2698 10016 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2699 10017 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2700 10018 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
2701 10019 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
2702 10020 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
2703 10021 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
2704 10022 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
2705 10023 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
2706 10024 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
2707 10025 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
2708 10026 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
2709 10027 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
2710 10028 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
2717 10035 9.892130 AGCTCTAATACAAATTTGTACTAAGCT 57.108 29.630 30.24 30.24 45.47 3.74
2722 10040 9.819267 GGACTAGCTCTAATACAAATTTGTACT 57.181 33.333 28.62 22.27 45.47 2.73
2723 10041 9.595823 TGGACTAGCTCTAATACAAATTTGTAC 57.404 33.333 28.62 16.82 45.47 2.90
2725 10043 9.515226 TTTGGACTAGCTCTAATACAAATTTGT 57.485 29.630 25.99 25.99 44.86 2.83
2726 10044 9.994432 CTTTGGACTAGCTCTAATACAAATTTG 57.006 33.333 16.67 16.67 0.00 2.32
2727 10045 9.740710 ACTTTGGACTAGCTCTAATACAAATTT 57.259 29.630 0.00 0.00 0.00 1.82
2728 10046 9.740710 AACTTTGGACTAGCTCTAATACAAATT 57.259 29.630 0.00 0.00 0.00 1.82
2729 10047 9.167311 CAACTTTGGACTAGCTCTAATACAAAT 57.833 33.333 0.00 0.00 0.00 2.32
2730 10048 8.372459 TCAACTTTGGACTAGCTCTAATACAAA 58.628 33.333 0.00 0.00 0.00 2.83
2731 10049 7.903145 TCAACTTTGGACTAGCTCTAATACAA 58.097 34.615 0.00 0.00 0.00 2.41
2732 10050 7.396339 TCTCAACTTTGGACTAGCTCTAATACA 59.604 37.037 0.00 0.00 0.00 2.29
2733 10051 7.703197 GTCTCAACTTTGGACTAGCTCTAATAC 59.297 40.741 0.00 0.00 0.00 1.89
2734 10052 7.396339 TGTCTCAACTTTGGACTAGCTCTAATA 59.604 37.037 0.00 0.00 32.88 0.98
2735 10053 6.211584 TGTCTCAACTTTGGACTAGCTCTAAT 59.788 38.462 0.00 0.00 32.88 1.73
2736 10054 5.538813 TGTCTCAACTTTGGACTAGCTCTAA 59.461 40.000 0.00 0.00 32.88 2.10
2737 10055 5.047943 GTGTCTCAACTTTGGACTAGCTCTA 60.048 44.000 0.00 0.00 32.88 2.43
2738 10056 3.898123 TGTCTCAACTTTGGACTAGCTCT 59.102 43.478 0.00 0.00 32.88 4.09
2739 10057 3.991121 GTGTCTCAACTTTGGACTAGCTC 59.009 47.826 0.00 0.00 32.88 4.09
2740 10058 3.643792 AGTGTCTCAACTTTGGACTAGCT 59.356 43.478 0.00 0.00 32.88 3.32
2741 10059 3.996480 AGTGTCTCAACTTTGGACTAGC 58.004 45.455 10.17 0.00 32.88 3.42
2742 10060 8.608844 AAATAAGTGTCTCAACTTTGGACTAG 57.391 34.615 10.17 0.00 40.77 2.57
2743 10061 8.836413 CAAAATAAGTGTCTCAACTTTGGACTA 58.164 33.333 10.17 0.00 40.77 2.59
2744 10062 7.201821 CCAAAATAAGTGTCTCAACTTTGGACT 60.202 37.037 4.59 0.00 40.77 3.85
2745 10063 6.918022 CCAAAATAAGTGTCTCAACTTTGGAC 59.082 38.462 4.59 4.53 40.77 4.02
2746 10064 6.040391 CCCAAAATAAGTGTCTCAACTTTGGA 59.960 38.462 10.94 0.00 40.77 3.53
2747 10065 6.040391 TCCCAAAATAAGTGTCTCAACTTTGG 59.960 38.462 0.00 0.00 40.77 3.28
2748 10066 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2749 10067 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2750 10068 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2751 10069 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2752 10070 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2753 10071 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2754 10072 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2755 10073 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2756 10074 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2757 10075 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2758 10076 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2759 10077 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2760 10078 2.271777 TCCCTCCGTCCCAAAATAAGT 58.728 47.619 0.00 0.00 0.00 2.24
2761 10079 3.359695 TTCCCTCCGTCCCAAAATAAG 57.640 47.619 0.00 0.00 0.00 1.73
2762 10080 5.656549 ATATTCCCTCCGTCCCAAAATAA 57.343 39.130 0.00 0.00 0.00 1.40
2763 10081 5.656549 AATATTCCCTCCGTCCCAAAATA 57.343 39.130 0.00 0.00 0.00 1.40
2764 10082 4.536295 AATATTCCCTCCGTCCCAAAAT 57.464 40.909 0.00 0.00 0.00 1.82
2765 10083 5.453866 TTAATATTCCCTCCGTCCCAAAA 57.546 39.130 0.00 0.00 0.00 2.44
2766 10084 5.656549 ATTAATATTCCCTCCGTCCCAAA 57.343 39.130 0.00 0.00 0.00 3.28
2767 10085 5.656549 AATTAATATTCCCTCCGTCCCAA 57.343 39.130 0.00 0.00 0.00 4.12
2768 10086 6.746043 GCTTAATTAATATTCCCTCCGTCCCA 60.746 42.308 0.00 0.00 0.00 4.37
2769 10087 5.646793 GCTTAATTAATATTCCCTCCGTCCC 59.353 44.000 0.00 0.00 0.00 4.46
2770 10088 6.473758 AGCTTAATTAATATTCCCTCCGTCC 58.526 40.000 0.00 0.00 0.00 4.79
2771 10089 7.660208 TCAAGCTTAATTAATATTCCCTCCGTC 59.340 37.037 0.00 0.00 0.00 4.79
2772 10090 7.514721 TCAAGCTTAATTAATATTCCCTCCGT 58.485 34.615 0.00 0.00 0.00 4.69
2773 10091 7.979444 TCAAGCTTAATTAATATTCCCTCCG 57.021 36.000 0.00 0.00 0.00 4.63
2774 10092 8.577296 GGTTCAAGCTTAATTAATATTCCCTCC 58.423 37.037 0.00 0.00 0.00 4.30
2775 10093 9.131791 TGGTTCAAGCTTAATTAATATTCCCTC 57.868 33.333 0.00 0.00 0.00 4.30
2776 10094 9.660544 ATGGTTCAAGCTTAATTAATATTCCCT 57.339 29.630 0.00 0.00 0.00 4.20
2801 10119 6.084326 AGTTTCGACACCAAGCATTTAAAT 57.916 33.333 0.00 0.00 0.00 1.40
2861 10179 9.800433 CATTTATTTATTCTGCACATACCAACA 57.200 29.630 0.00 0.00 0.00 3.33
2887 10205 9.985318 GCAGCAACTTCTATTATATCATCAATC 57.015 33.333 0.00 0.00 0.00 2.67
2933 10251 0.396974 AACAACACTGGGCCACACAT 60.397 50.000 0.00 0.00 0.00 3.21
2958 10276 0.892755 ATGACGAGTTCGCCTTACCA 59.107 50.000 0.73 0.00 44.43 3.25
2996 10315 2.039084 ACCACCACCAACTCAGATCTTC 59.961 50.000 0.00 0.00 0.00 2.87
3167 10487 8.762426 GTTAAACGTTTCTGTCATCTTAGTCTT 58.238 33.333 18.42 0.00 0.00 3.01
3174 10494 7.924412 TGAGTTAGTTAAACGTTTCTGTCATCT 59.076 33.333 18.42 9.13 43.29 2.90


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

AutoCloner maintained by Alex Coulton.