Multiple sequence alignment - TraesCS5B01G444300

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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 TraesCS5B01G444300 chr5B 100.000 3486 0 0 1402 4887 616975243 616971758 0.000000e+00 6438.0
1 TraesCS5B01G444300 chr5B 100.000 1073 0 0 1 1073 616976644 616975572 0.000000e+00 1982.0
2 TraesCS5B01G444300 chr5B 89.024 246 27 0 3662 3907 616967620 616967375 6.150000e-79 305.0
3 TraesCS5B01G444300 chr5B 88.889 45 5 0 3613 3657 617175583 617175539 6.830000e-04 56.5
4 TraesCS5B01G444300 chr5D 94.076 2954 105 28 1605 4516 497831771 497828846 0.000000e+00 4421.0
5 TraesCS5B01G444300 chr5D 96.809 376 10 2 4512 4887 497828818 497828445 1.150000e-175 627.0
6 TraesCS5B01G444300 chr5D 88.924 316 22 8 759 1066 497832677 497832367 1.280000e-100 377.0
7 TraesCS5B01G444300 chr5A 91.447 1894 76 23 2667 4516 621857388 621855537 0.000000e+00 2521.0
8 TraesCS5B01G444300 chr5A 94.857 1011 44 7 1657 2662 621859512 621858505 0.000000e+00 1572.0
9 TraesCS5B01G444300 chr5A 90.000 380 16 4 4512 4887 621855509 621855148 5.730000e-129 472.0
10 TraesCS5B01G444300 chr5A 91.065 291 14 6 772 1062 621860487 621860209 2.760000e-102 383.0
11 TraesCS5B01G444300 chr5A 90.179 112 1 2 1455 1566 621859728 621859627 2.370000e-28 137.0
12 TraesCS5B01G444300 chr5A 86.364 66 3 1 1568 1627 621859572 621859507 3.160000e-07 67.6
13 TraesCS5B01G444300 chr6B 96.779 745 19 4 1 743 525184594 525185335 0.000000e+00 1238.0
14 TraesCS5B01G444300 chr6B 94.533 750 28 4 1 743 664721795 664722538 0.000000e+00 1146.0
15 TraesCS5B01G444300 chr2B 96.515 746 22 3 1 744 170087963 170088706 0.000000e+00 1230.0
16 TraesCS5B01G444300 chr2B 96.237 744 27 1 1 743 12170489 12169746 0.000000e+00 1218.0
17 TraesCS5B01G444300 chr2B 95.298 319 13 2 428 744 28341645 28341963 5.650000e-139 505.0
18 TraesCS5B01G444300 chr3B 96.242 745 24 3 1 743 506733309 506732567 0.000000e+00 1218.0
19 TraesCS5B01G444300 chr3B 96.545 550 15 3 1 548 506735470 506736017 0.000000e+00 907.0
20 TraesCS5B01G444300 chr3B 92.122 622 21 7 1 620 160122820 160122225 0.000000e+00 852.0
21 TraesCS5B01G444300 chr7B 97.046 711 21 0 36 746 579821902 579821192 0.000000e+00 1197.0
22 TraesCS5B01G444300 chr7B 97.125 626 17 1 1 625 742603220 742603845 0.000000e+00 1055.0
23 TraesCS5B01G444300 chr4A 91.250 400 22 7 350 744 465216192 465215801 2.590000e-147 532.0
24 TraesCS5B01G444300 chr2A 89.826 403 30 5 350 747 197229371 197228975 1.570000e-139 507.0


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 TraesCS5B01G444300 chr5B 616971758 616976644 4886 True 4210.000000 6438 100.000000 1 4887 2 chr5B.!!$R3 4886
1 TraesCS5B01G444300 chr5D 497828445 497832677 4232 True 1808.333333 4421 93.269667 759 4887 3 chr5D.!!$R1 4128
2 TraesCS5B01G444300 chr5A 621855148 621860487 5339 True 858.766667 2521 90.652000 772 4887 6 chr5A.!!$R1 4115
3 TraesCS5B01G444300 chr6B 525184594 525185335 741 False 1238.000000 1238 96.779000 1 743 1 chr6B.!!$F1 742
4 TraesCS5B01G444300 chr6B 664721795 664722538 743 False 1146.000000 1146 94.533000 1 743 1 chr6B.!!$F2 742
5 TraesCS5B01G444300 chr2B 170087963 170088706 743 False 1230.000000 1230 96.515000 1 744 1 chr2B.!!$F2 743
6 TraesCS5B01G444300 chr2B 12169746 12170489 743 True 1218.000000 1218 96.237000 1 743 1 chr2B.!!$R1 742
7 TraesCS5B01G444300 chr3B 506732567 506733309 742 True 1218.000000 1218 96.242000 1 743 1 chr3B.!!$R2 742
8 TraesCS5B01G444300 chr3B 506735470 506736017 547 False 907.000000 907 96.545000 1 548 1 chr3B.!!$F1 547
9 TraesCS5B01G444300 chr3B 160122225 160122820 595 True 852.000000 852 92.122000 1 620 1 chr3B.!!$R1 619
10 TraesCS5B01G444300 chr7B 579821192 579821902 710 True 1197.000000 1197 97.046000 36 746 1 chr7B.!!$R1 710
11 TraesCS5B01G444300 chr7B 742603220 742603845 625 False 1055.000000 1055 97.125000 1 625 1 chr7B.!!$F1 624

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
783 829 0.179097 TGTTTTGTTTTGAGGCGGCC 60.179 50.000 12.11 12.11 0.00 6.13 F
872 919 0.519077 CCCACTCGCTCTGCTTTTTC 59.481 55.000 0.00 0.00 0.00 2.29 F
1451 1676 1.070601 AGGAAATTTGCTGTGTTGCCC 59.929 47.619 11.84 0.00 0.00 5.36 F
1452 1677 1.070601 GGAAATTTGCTGTGTTGCCCT 59.929 47.619 1.93 0.00 0.00 5.19 F
1749 2035 1.303236 CCCTGATTTGGCGACCACA 60.303 57.895 0.00 0.00 30.78 4.17 F
1752 2039 1.452110 CTGATTTGGCGACCACATCA 58.548 50.000 19.61 19.61 45.05 3.07 F
1761 2048 1.577328 CGACCACATCAAAGGCGCTT 61.577 55.000 7.64 0.00 0.00 4.68 F
2331 2618 2.291865 ACATAGAGCTGGTGAGTCCTCA 60.292 50.000 0.00 0.00 37.24 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1905 0.170116 CCCAACACACACACACACAC 59.830 55.000 0.0 0.00 0.00 3.82 R
2707 4111 1.279496 AGTGCAGCCTGATCAACCTA 58.721 50.000 0.0 0.00 0.00 3.08 R
3389 4805 0.979665 ACAGCACTCACCTGCATAGT 59.020 50.000 0.0 0.00 39.86 2.12 R
3390 4806 1.649664 GACAGCACTCACCTGCATAG 58.350 55.000 0.0 0.00 39.86 2.23 R
3461 4877 2.165998 GCAAACCTGCTTGATCTCCTT 58.834 47.619 0.0 0.00 45.74 3.36 R
3736 5152 4.342772 CCGCAATCTGTATTACAAACAGC 58.657 43.478 0.0 0.48 43.30 4.40 R
3826 5242 6.783708 TCTATTCTTCTCAGTCCTTCTTCC 57.216 41.667 0.0 0.00 0.00 3.46 R
3892 5308 2.416431 GGCTTGTTCATGATGGAACTGC 60.416 50.000 0.0 10.39 45.74 4.40 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
49 88 4.564769 GTCCGTGCTTTCAAAAATTGTTCA 59.435 37.500 0.00 0.00 0.00 3.18
488 528 9.419297 GATGTTCACTACAGTGTGTAATTCTAA 57.581 33.333 5.88 0.00 45.76 2.10
605 645 2.087009 GTCGCAGGTTCGAGTTCGG 61.087 63.158 1.26 0.00 39.34 4.30
626 672 1.134907 GTTTCCATCGCGTCTCCCTTA 60.135 52.381 5.77 0.00 0.00 2.69
746 792 2.289195 CGTCCTATAGGAGCTCTCGAGT 60.289 54.545 22.30 0.00 46.49 4.18
747 793 3.056678 CGTCCTATAGGAGCTCTCGAGTA 60.057 52.174 22.30 0.00 46.49 2.59
748 794 4.501071 GTCCTATAGGAGCTCTCGAGTAG 58.499 52.174 22.30 9.69 46.49 2.57
749 795 4.221262 GTCCTATAGGAGCTCTCGAGTAGA 59.779 50.000 22.30 0.32 46.49 2.59
750 796 4.839550 TCCTATAGGAGCTCTCGAGTAGAA 59.160 45.833 18.00 0.00 39.78 2.10
751 797 5.046878 TCCTATAGGAGCTCTCGAGTAGAAG 60.047 48.000 18.00 3.22 39.78 2.85
752 798 4.699925 ATAGGAGCTCTCGAGTAGAAGT 57.300 45.455 14.64 0.00 32.46 3.01
753 799 5.811796 ATAGGAGCTCTCGAGTAGAAGTA 57.188 43.478 14.64 0.00 32.46 2.24
754 800 4.699925 AGGAGCTCTCGAGTAGAAGTAT 57.300 45.455 14.64 0.00 32.46 2.12
755 801 4.385825 AGGAGCTCTCGAGTAGAAGTATG 58.614 47.826 14.64 0.00 32.46 2.39
756 802 4.101898 AGGAGCTCTCGAGTAGAAGTATGA 59.898 45.833 14.64 0.00 32.46 2.15
757 803 4.817464 GGAGCTCTCGAGTAGAAGTATGAA 59.183 45.833 14.64 0.00 32.46 2.57
758 804 5.472137 GGAGCTCTCGAGTAGAAGTATGAAT 59.528 44.000 14.64 0.00 32.46 2.57
759 805 6.348213 GGAGCTCTCGAGTAGAAGTATGAATC 60.348 46.154 14.64 0.00 32.46 2.52
760 806 6.296026 AGCTCTCGAGTAGAAGTATGAATCT 58.704 40.000 13.13 0.00 32.46 2.40
761 807 6.770785 AGCTCTCGAGTAGAAGTATGAATCTT 59.229 38.462 13.13 0.00 32.46 2.40
762 808 7.284489 AGCTCTCGAGTAGAAGTATGAATCTTT 59.716 37.037 13.13 0.00 32.46 2.52
763 809 7.918562 GCTCTCGAGTAGAAGTATGAATCTTTT 59.081 37.037 13.13 0.00 32.46 2.27
764 810 9.796120 CTCTCGAGTAGAAGTATGAATCTTTTT 57.204 33.333 13.13 0.00 32.46 1.94
765 811 9.574458 TCTCGAGTAGAAGTATGAATCTTTTTG 57.426 33.333 13.13 0.00 0.00 2.44
766 812 9.360093 CTCGAGTAGAAGTATGAATCTTTTTGT 57.640 33.333 3.62 0.00 0.00 2.83
767 813 9.706691 TCGAGTAGAAGTATGAATCTTTTTGTT 57.293 29.630 0.00 0.00 0.00 2.83
783 829 0.179097 TGTTTTGTTTTGAGGCGGCC 60.179 50.000 12.11 12.11 0.00 6.13
792 838 4.329545 GAGGCGGCCACCTTGTGA 62.330 66.667 23.09 0.00 41.32 3.58
798 844 2.282040 GCCACCTTGTGAGCTGCT 60.282 61.111 0.00 0.00 35.23 4.24
845 891 1.526917 CCCGGCCTGCTAATCCAAG 60.527 63.158 0.00 0.00 0.00 3.61
872 919 0.519077 CCCACTCGCTCTGCTTTTTC 59.481 55.000 0.00 0.00 0.00 2.29
880 927 2.810852 CGCTCTGCTTTTTCTTCTTCCT 59.189 45.455 0.00 0.00 0.00 3.36
881 928 3.120373 CGCTCTGCTTTTTCTTCTTCCTC 60.120 47.826 0.00 0.00 0.00 3.71
888 935 4.324267 CTTTTTCTTCTTCCTCCGGCTTA 58.676 43.478 0.00 0.00 0.00 3.09
1069 1123 2.047274 GCGGCAAGGTGCTCACTA 60.047 61.111 0.00 0.00 44.28 2.74
1070 1124 1.450312 GCGGCAAGGTGCTCACTAT 60.450 57.895 0.00 0.00 44.28 2.12
1071 1125 1.709147 GCGGCAAGGTGCTCACTATG 61.709 60.000 0.00 1.47 44.28 2.23
1072 1126 1.709147 CGGCAAGGTGCTCACTATGC 61.709 60.000 16.44 16.44 44.28 3.14
1427 1612 4.324267 AGCGAACTAAGTATGGTTGCTTT 58.676 39.130 0.00 0.00 33.80 3.51
1429 1614 4.671766 GCGAACTAAGTATGGTTGCTTTGG 60.672 45.833 0.00 0.00 29.37 3.28
1441 1666 1.881591 TGCTTTGGCAGGAAATTTGC 58.118 45.000 0.68 0.68 44.28 3.68
1442 1667 1.417145 TGCTTTGGCAGGAAATTTGCT 59.583 42.857 6.36 6.36 44.28 3.91
1444 1669 2.807837 GCTTTGGCAGGAAATTTGCTGT 60.808 45.455 32.04 3.75 46.76 4.40
1445 1670 2.529780 TTGGCAGGAAATTTGCTGTG 57.470 45.000 32.04 15.85 46.76 3.66
1446 1671 1.412079 TGGCAGGAAATTTGCTGTGT 58.588 45.000 32.04 2.68 46.76 3.72
1447 1672 1.761784 TGGCAGGAAATTTGCTGTGTT 59.238 42.857 32.04 2.32 46.76 3.32
1448 1673 2.137523 GGCAGGAAATTTGCTGTGTTG 58.862 47.619 32.04 14.58 46.76 3.33
1449 1674 1.528161 GCAGGAAATTTGCTGTGTTGC 59.472 47.619 32.04 19.55 46.76 4.17
1450 1675 2.137523 CAGGAAATTTGCTGTGTTGCC 58.862 47.619 26.46 5.25 41.12 4.52
1451 1676 1.070601 AGGAAATTTGCTGTGTTGCCC 59.929 47.619 11.84 0.00 0.00 5.36
1452 1677 1.070601 GGAAATTTGCTGTGTTGCCCT 59.929 47.619 1.93 0.00 0.00 5.19
1453 1678 2.137523 GAAATTTGCTGTGTTGCCCTG 58.862 47.619 0.00 0.00 0.00 4.45
1473 1698 1.466360 GCTAATTCAGGTGCACAAGCG 60.466 52.381 20.43 3.36 46.23 4.68
1496 1721 4.928398 CTGCGACAGCCTGAATCT 57.072 55.556 0.00 0.00 44.33 2.40
1566 1793 2.755103 GTTTCTTACCAGAGGCCAATGG 59.245 50.000 21.44 21.44 42.60 3.16
1619 1905 4.037565 AGGATGTCAGCATTGCACATATTG 59.962 41.667 11.91 0.00 35.07 1.90
1621 1907 4.678622 ATGTCAGCATTGCACATATTGTG 58.321 39.130 11.91 3.29 40.82 3.33
1634 1920 3.944650 ACATATTGTGTGTGTGTGTGTGT 59.055 39.130 0.00 0.00 40.28 3.72
1646 1932 4.614036 GTGTGTTGGGGGTGGGGG 62.614 72.222 0.00 0.00 0.00 5.40
1647 1933 4.865228 TGTGTTGGGGGTGGGGGA 62.865 66.667 0.00 0.00 0.00 4.81
1749 2035 1.303236 CCCTGATTTGGCGACCACA 60.303 57.895 0.00 0.00 30.78 4.17
1752 2039 1.452110 CTGATTTGGCGACCACATCA 58.548 50.000 19.61 19.61 45.05 3.07
1761 2048 1.577328 CGACCACATCAAAGGCGCTT 61.577 55.000 7.64 0.00 0.00 4.68
1821 2108 2.728817 GTGCCCTACTCGGATCCG 59.271 66.667 28.62 28.62 41.35 4.18
1858 2145 3.260884 AGTCATTCAGGTACATGTTCCGT 59.739 43.478 15.04 2.30 0.00 4.69
1915 2202 4.202101 TGTCATTGGGCTACAAGTGTTTTG 60.202 41.667 0.00 0.00 43.48 2.44
2066 2353 7.613585 TCACATACTACAACCCGATTCTAAAA 58.386 34.615 0.00 0.00 0.00 1.52
2133 2420 9.310716 GTGTACATGGTATCTTTTCTTACTACC 57.689 37.037 0.00 0.00 33.86 3.18
2191 2478 4.307432 TGCTCTTGTTACTAGTTGCTGTC 58.693 43.478 0.00 0.00 0.00 3.51
2192 2479 4.202212 TGCTCTTGTTACTAGTTGCTGTCA 60.202 41.667 0.00 0.00 0.00 3.58
2201 2488 5.157940 ACTAGTTGCTGTCATTGATCTGT 57.842 39.130 0.00 0.00 0.00 3.41
2232 2519 7.992180 TCTTCTGAAAAGTTTGATTTGCTTC 57.008 32.000 0.00 0.00 0.00 3.86
2330 2617 2.383855 ACATAGAGCTGGTGAGTCCTC 58.616 52.381 0.00 0.00 37.07 3.71
2331 2618 2.291865 ACATAGAGCTGGTGAGTCCTCA 60.292 50.000 0.00 0.00 37.24 3.86
2363 2650 5.993106 TGTCATGTAATGTTCGTGTGAAA 57.007 34.783 0.00 0.00 46.80 2.69
2737 4141 2.756400 CTGCACTAGGTGGGCCAA 59.244 61.111 8.40 0.00 46.54 4.52
2826 4235 6.261603 GTCATGAACTATCCATGCATTGAAGA 59.738 38.462 4.35 0.00 40.74 2.87
2870 4279 7.455638 TGTTACCTACACTACCTGGTTAGAATT 59.544 37.037 3.84 0.00 34.33 2.17
2876 4285 7.490657 ACACTACCTGGTTAGAATTGTATCA 57.509 36.000 3.84 0.00 0.00 2.15
3115 4525 8.559536 TGTCACTAGATTCAAACAACATTTCTC 58.440 33.333 0.00 0.00 0.00 2.87
3218 4628 7.999679 ACACACCATATAATTTGTCATCTTGG 58.000 34.615 0.00 0.00 0.00 3.61
3219 4629 7.068593 ACACACCATATAATTTGTCATCTTGGG 59.931 37.037 0.00 0.00 0.00 4.12
3220 4630 6.550854 ACACCATATAATTTGTCATCTTGGGG 59.449 38.462 0.00 0.00 0.00 4.96
3221 4631 5.539955 ACCATATAATTTGTCATCTTGGGGC 59.460 40.000 0.00 0.00 0.00 5.80
3222 4632 5.776716 CCATATAATTTGTCATCTTGGGGCT 59.223 40.000 0.00 0.00 0.00 5.19
3354 4766 5.760253 CCTCATGTTACATCAACCCTGATAC 59.240 44.000 0.00 0.00 40.49 2.24
3367 4783 8.528044 TCAACCCTGATACTTTTTAAACACTT 57.472 30.769 0.00 0.00 0.00 3.16
3389 4805 8.935844 CACTTGATTTGTTAACTAGCTCATACA 58.064 33.333 7.22 0.00 0.00 2.29
3390 4806 8.936864 ACTTGATTTGTTAACTAGCTCATACAC 58.063 33.333 7.22 0.00 0.00 2.90
3726 5142 6.872920 TGGTCTATCTTTTGTTGCAAGTTTT 58.127 32.000 0.00 0.00 0.00 2.43
3736 5152 6.586868 TTGTTGCAAGTTTTGATAGCTTTG 57.413 33.333 0.00 0.00 0.00 2.77
3754 5170 7.219484 AGCTTTGCTGTTTGTAATACAGATT 57.781 32.000 7.15 0.00 44.52 2.40
3874 5290 2.796651 GCCAAGAGCATCAAGGCG 59.203 61.111 0.00 0.00 45.03 5.52
3959 5375 5.127194 TCGTTTATCATCTGGTAGTCTGCTT 59.873 40.000 0.00 0.00 0.00 3.91
3974 5390 2.092753 TCTGCTTGATGGACCTGGAATC 60.093 50.000 0.00 1.28 0.00 2.52
3982 5398 4.162320 TGATGGACCTGGAATCTGTAGTTC 59.838 45.833 0.00 0.00 0.00 3.01
3987 5403 3.193691 ACCTGGAATCTGTAGTTCGTCTG 59.806 47.826 0.00 0.00 0.00 3.51
4021 5437 8.970020 TGATTCCAGTGCTCAAAACAATTATAT 58.030 29.630 0.00 0.00 0.00 0.86
4085 5501 3.195661 GGAAATGGTACGAAGCTCGATT 58.804 45.455 11.64 0.00 43.74 3.34
4086 5502 3.621715 GGAAATGGTACGAAGCTCGATTT 59.378 43.478 11.64 2.89 43.74 2.17
4087 5503 4.260253 GGAAATGGTACGAAGCTCGATTTC 60.260 45.833 11.64 10.63 43.74 2.17
4088 5504 3.802948 ATGGTACGAAGCTCGATTTCT 57.197 42.857 11.64 0.00 43.74 2.52
4089 5505 2.876091 TGGTACGAAGCTCGATTTCTG 58.124 47.619 11.64 4.95 43.74 3.02
4090 5506 2.230508 TGGTACGAAGCTCGATTTCTGT 59.769 45.455 11.64 9.05 43.74 3.41
4091 5507 3.251571 GGTACGAAGCTCGATTTCTGTT 58.748 45.455 11.64 0.00 43.74 3.16
4092 5508 3.060895 GGTACGAAGCTCGATTTCTGTTG 59.939 47.826 11.64 0.00 43.74 3.33
4093 5509 2.755650 ACGAAGCTCGATTTCTGTTGT 58.244 42.857 11.64 0.00 43.74 3.32
4094 5510 2.476619 ACGAAGCTCGATTTCTGTTGTG 59.523 45.455 11.64 0.00 43.74 3.33
4095 5511 2.731451 CGAAGCTCGATTTCTGTTGTGA 59.269 45.455 7.83 0.00 43.74 3.58
4096 5512 3.181536 CGAAGCTCGATTTCTGTTGTGAG 60.182 47.826 7.83 0.00 43.74 3.51
4097 5513 2.693069 AGCTCGATTTCTGTTGTGAGG 58.307 47.619 0.00 0.00 0.00 3.86
4101 5543 4.611581 GCTCGATTTCTGTTGTGAGGAAAC 60.612 45.833 0.00 0.00 32.84 2.78
4126 5568 8.097038 ACATTGTGAGATGTAGTGTTCTTATGT 58.903 33.333 0.00 0.00 38.43 2.29
4280 5730 3.055240 CACTGCCCTCAGATTCTTCTTCT 60.055 47.826 0.00 0.00 42.95 2.85
4452 5903 6.697019 GTCAAACATTTTATGCGCCATTAGAT 59.303 34.615 4.18 0.00 0.00 1.98
4453 5904 7.222611 GTCAAACATTTTATGCGCCATTAGATT 59.777 33.333 4.18 0.00 0.00 2.40
4477 5928 0.976641 TCTCCGGACAGATGCTTTGT 59.023 50.000 0.00 0.00 0.00 2.83
4494 5945 9.185192 GATGCTTTGTTACAATATAATTCTGGC 57.815 33.333 0.00 0.00 0.00 4.85
4501 5952 7.965655 TGTTACAATATAATTCTGGCGTGTTTG 59.034 33.333 0.00 0.00 0.00 2.93
4744 6231 3.056832 AGACCTTTCCCTTTCCTGAACT 58.943 45.455 0.00 0.00 0.00 3.01
4752 6239 2.224621 CCCTTTCCTGAACTGAGCAGAA 60.225 50.000 4.21 0.00 35.39 3.02
4790 6277 8.908786 TCTATGGACCATGACATTAGAAAATC 57.091 34.615 17.73 0.00 0.00 2.17
4858 6345 5.945310 AGGAATATACACATGCATCCAAGT 58.055 37.500 0.00 0.00 0.00 3.16
4863 6350 1.895131 ACACATGCATCCAAGTTTCCC 59.105 47.619 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 48 5.462034 TTGAACAATTTTTGAAAGCACGG 57.538 34.783 0.00 0.00 0.00 4.94
49 88 8.596293 TGAAATGGAGAATAAATTTGGAAGCTT 58.404 29.630 0.00 0.00 0.00 3.74
63 102 9.835389 TTGAGAACAAATTTTGAAATGGAGAAT 57.165 25.926 15.81 0.00 32.73 2.40
406 446 7.540745 GTGTATATTTTGAAAAAGTGCGACCAT 59.459 33.333 0.00 0.00 0.00 3.55
488 528 8.550710 TTAATAACTTAGCACAACCGTACAAT 57.449 30.769 0.00 0.00 0.00 2.71
581 621 0.456221 CTCGAACCTGCGACCTACAT 59.544 55.000 0.00 0.00 36.17 2.29
605 645 1.814169 GGGAGACGCGATGGAAACC 60.814 63.158 15.93 5.91 0.00 3.27
626 672 5.419542 GTGAGAAAAGAAAGCAAAAAGGGT 58.580 37.500 0.00 0.00 0.00 4.34
753 799 8.183536 GCCTCAAAACAAAACAAAAAGATTCAT 58.816 29.630 0.00 0.00 0.00 2.57
754 800 7.525759 GCCTCAAAACAAAACAAAAAGATTCA 58.474 30.769 0.00 0.00 0.00 2.57
755 801 6.682441 CGCCTCAAAACAAAACAAAAAGATTC 59.318 34.615 0.00 0.00 0.00 2.52
756 802 6.403092 CCGCCTCAAAACAAAACAAAAAGATT 60.403 34.615 0.00 0.00 0.00 2.40
757 803 5.064579 CCGCCTCAAAACAAAACAAAAAGAT 59.935 36.000 0.00 0.00 0.00 2.40
758 804 4.390297 CCGCCTCAAAACAAAACAAAAAGA 59.610 37.500 0.00 0.00 0.00 2.52
759 805 4.646960 CCGCCTCAAAACAAAACAAAAAG 58.353 39.130 0.00 0.00 0.00 2.27
760 806 3.120165 GCCGCCTCAAAACAAAACAAAAA 60.120 39.130 0.00 0.00 0.00 1.94
761 807 2.416893 GCCGCCTCAAAACAAAACAAAA 59.583 40.909 0.00 0.00 0.00 2.44
762 808 2.003301 GCCGCCTCAAAACAAAACAAA 58.997 42.857 0.00 0.00 0.00 2.83
763 809 1.646189 GCCGCCTCAAAACAAAACAA 58.354 45.000 0.00 0.00 0.00 2.83
764 810 0.179097 GGCCGCCTCAAAACAAAACA 60.179 50.000 0.71 0.00 0.00 2.83
765 811 0.179097 TGGCCGCCTCAAAACAAAAC 60.179 50.000 11.61 0.00 0.00 2.43
766 812 0.179097 GTGGCCGCCTCAAAACAAAA 60.179 50.000 11.61 0.00 0.00 2.44
767 813 1.439644 GTGGCCGCCTCAAAACAAA 59.560 52.632 11.61 0.00 0.00 2.83
768 814 2.494530 GGTGGCCGCCTCAAAACAA 61.495 57.895 28.79 0.00 0.00 2.83
769 815 2.909965 GGTGGCCGCCTCAAAACA 60.910 61.111 28.79 0.00 0.00 2.83
770 816 2.200337 AAGGTGGCCGCCTCAAAAC 61.200 57.895 37.53 7.78 38.03 2.43
860 906 3.190327 GGAGGAAGAAGAAAAAGCAGAGC 59.810 47.826 0.00 0.00 0.00 4.09
880 927 1.137404 GCGTCGTAACTAAGCCGGA 59.863 57.895 5.05 0.00 0.00 5.14
881 928 2.219562 CGCGTCGTAACTAAGCCGG 61.220 63.158 0.00 0.00 0.00 6.13
1427 1612 1.412079 ACACAGCAAATTTCCTGCCA 58.588 45.000 9.10 0.00 40.86 4.92
1429 1614 1.528161 GCAACACAGCAAATTTCCTGC 59.472 47.619 9.10 0.46 40.24 4.85
1439 1664 0.251297 ATTAGCAGGGCAACACAGCA 60.251 50.000 0.00 0.00 39.74 4.41
1440 1665 0.890683 AATTAGCAGGGCAACACAGC 59.109 50.000 0.00 0.00 39.74 4.40
1441 1666 2.161855 TGAATTAGCAGGGCAACACAG 58.838 47.619 0.00 0.00 39.74 3.66
1442 1667 2.161855 CTGAATTAGCAGGGCAACACA 58.838 47.619 0.00 0.00 39.74 3.72
1443 1668 2.927553 CTGAATTAGCAGGGCAACAC 57.072 50.000 0.00 0.00 39.74 3.32
1451 1676 2.415090 GCTTGTGCACCTGAATTAGCAG 60.415 50.000 15.69 0.00 37.72 4.24
1452 1677 1.541147 GCTTGTGCACCTGAATTAGCA 59.459 47.619 15.69 0.00 39.41 3.49
1453 1678 1.466360 CGCTTGTGCACCTGAATTAGC 60.466 52.381 15.69 10.19 39.64 3.09
1480 1705 2.034878 AGATAGATTCAGGCTGTCGCA 58.965 47.619 15.27 0.00 38.10 5.10
1483 1708 6.437162 AGAGGAATAGATAGATTCAGGCTGTC 59.563 42.308 15.27 5.65 37.53 3.51
1484 1709 6.322126 AGAGGAATAGATAGATTCAGGCTGT 58.678 40.000 15.27 0.00 37.53 4.40
1485 1710 6.436847 TGAGAGGAATAGATAGATTCAGGCTG 59.563 42.308 8.58 8.58 37.53 4.85
1487 1712 6.849085 TGAGAGGAATAGATAGATTCAGGC 57.151 41.667 0.00 0.00 37.53 4.85
1488 1713 9.919416 TCTATGAGAGGAATAGATAGATTCAGG 57.081 37.037 0.00 0.00 37.53 3.86
1570 1850 2.224090 TGTGCTAGTACTGTTTTCCGCA 60.224 45.455 12.42 0.26 0.00 5.69
1619 1905 0.170116 CCCAACACACACACACACAC 59.830 55.000 0.00 0.00 0.00 3.82
1621 1907 1.662438 CCCCCAACACACACACACAC 61.662 60.000 0.00 0.00 0.00 3.82
1651 1937 2.042569 ACCCTAAAATGAACCACCTCCC 59.957 50.000 0.00 0.00 0.00 4.30
1652 1938 3.089284 CACCCTAAAATGAACCACCTCC 58.911 50.000 0.00 0.00 0.00 4.30
1653 1939 3.763057 ACACCCTAAAATGAACCACCTC 58.237 45.455 0.00 0.00 0.00 3.85
1654 1940 3.895704 ACACCCTAAAATGAACCACCT 57.104 42.857 0.00 0.00 0.00 4.00
1655 1941 3.057806 CGAACACCCTAAAATGAACCACC 60.058 47.826 0.00 0.00 0.00 4.61
1689 1975 4.354587 GGATGAATGCCGTCTGAAAATTC 58.645 43.478 0.00 0.00 0.00 2.17
1749 2035 1.771255 AGGATCCTAAGCGCCTTTGAT 59.229 47.619 14.27 1.09 0.00 2.57
1752 2039 2.365941 GTCTAGGATCCTAAGCGCCTTT 59.634 50.000 21.93 0.00 32.04 3.11
1761 2048 2.570415 CGCAGGAGTCTAGGATCCTA 57.430 55.000 20.53 20.53 44.30 2.94
1821 2108 3.550437 ATGACTGGACCATCAGCTAAC 57.450 47.619 0.00 0.00 38.26 2.34
1915 2202 1.560505 ATGAAATGGCTGTGAACCCC 58.439 50.000 0.00 0.00 0.00 4.95
2066 2353 1.698506 TGAAGTTTCGCACCCCATTT 58.301 45.000 0.00 0.00 0.00 2.32
2072 2359 1.448985 TAGCCATGAAGTTTCGCACC 58.551 50.000 0.00 0.00 0.00 5.01
2078 2365 7.466746 TTGCTTAATCTTAGCCATGAAGTTT 57.533 32.000 0.00 0.00 37.85 2.66
2180 2467 6.492007 AAACAGATCAATGACAGCAACTAG 57.508 37.500 0.00 0.00 0.00 2.57
2209 2496 6.982724 AGGAAGCAAATCAAACTTTTCAGAAG 59.017 34.615 0.00 0.00 0.00 2.85
2216 2503 6.161381 CAGCATAGGAAGCAAATCAAACTTT 58.839 36.000 0.00 0.00 0.00 2.66
2219 2506 3.861689 GCAGCATAGGAAGCAAATCAAAC 59.138 43.478 0.00 0.00 0.00 2.93
2232 2519 1.661341 GACAAGACCTGCAGCATAGG 58.339 55.000 8.66 0.00 41.22 2.57
2330 2617 7.463780 CGAACATTACATGACAAGATGAGAGTG 60.464 40.741 0.00 0.00 0.00 3.51
2331 2618 6.533012 CGAACATTACATGACAAGATGAGAGT 59.467 38.462 0.00 0.00 0.00 3.24
2363 2650 6.365789 CGCCAATGACACAAATACAAGAAAAT 59.634 34.615 0.00 0.00 0.00 1.82
2557 2846 4.661222 TGAATGTGGCCTAGTCAAAATCA 58.339 39.130 3.32 2.99 0.00 2.57
2643 2934 3.063704 CCGCAGCAGGCCAAATCA 61.064 61.111 5.01 0.00 40.31 2.57
2684 4088 1.347707 CAGGCCTGAACTGGTCACTTA 59.652 52.381 29.88 0.00 33.35 2.24
2707 4111 1.279496 AGTGCAGCCTGATCAACCTA 58.721 50.000 0.00 0.00 0.00 3.08
2737 4141 5.700402 ATCAAGTAAACCTGAGCACCTAT 57.300 39.130 0.00 0.00 0.00 2.57
2809 4218 6.261603 TGTTTAGCTCTTCAATGCATGGATAG 59.738 38.462 4.15 7.07 0.00 2.08
2826 4235 4.357918 AACAGGTCAGTCATGTTTAGCT 57.642 40.909 0.00 0.00 46.71 3.32
2946 4356 6.094742 TGCAGCCAAGTGAAAATATAAATCGA 59.905 34.615 0.00 0.00 0.00 3.59
3115 4525 6.619801 ATTACTAAGCAAGGGATAAAAGCG 57.380 37.500 0.00 0.00 0.00 4.68
3216 4626 1.304891 AGTTATAAGCCCAAGCCCCA 58.695 50.000 0.00 0.00 41.25 4.96
3217 4627 2.307768 GAAGTTATAAGCCCAAGCCCC 58.692 52.381 0.00 0.00 41.25 5.80
3218 4628 2.307768 GGAAGTTATAAGCCCAAGCCC 58.692 52.381 0.00 0.00 41.25 5.19
3219 4629 2.091830 AGGGAAGTTATAAGCCCAAGCC 60.092 50.000 16.36 0.00 43.20 4.35
3220 4630 2.952310 CAGGGAAGTTATAAGCCCAAGC 59.048 50.000 16.36 0.00 43.20 4.01
3221 4631 3.202151 TCCAGGGAAGTTATAAGCCCAAG 59.798 47.826 16.36 10.20 43.20 3.61
3222 4632 3.194620 TCCAGGGAAGTTATAAGCCCAA 58.805 45.455 16.36 3.56 43.20 4.12
3303 4713 7.942341 TGAACATAACAGATAAAGTGACCCTTT 59.058 33.333 0.00 0.00 45.36 3.11
3374 4790 6.323996 ACCTGCATAGTGTATGAGCTAGTTAA 59.676 38.462 0.00 0.00 38.45 2.01
3389 4805 0.979665 ACAGCACTCACCTGCATAGT 59.020 50.000 0.00 0.00 39.86 2.12
3390 4806 1.649664 GACAGCACTCACCTGCATAG 58.350 55.000 0.00 0.00 39.86 2.23
3461 4877 2.165998 GCAAACCTGCTTGATCTCCTT 58.834 47.619 0.00 0.00 45.74 3.36
3589 5005 5.467063 GTCTGTAACCTGAAAACTCAAGGAG 59.533 44.000 0.00 0.00 35.52 3.69
3726 5142 7.606073 TCTGTATTACAAACAGCAAAGCTATCA 59.394 33.333 0.00 0.00 43.30 2.15
3736 5152 4.342772 CCGCAATCTGTATTACAAACAGC 58.657 43.478 0.00 0.48 43.30 4.40
3826 5242 6.783708 TCTATTCTTCTCAGTCCTTCTTCC 57.216 41.667 0.00 0.00 0.00 3.46
3835 5251 5.066764 GGCGTACTCTTCTATTCTTCTCAGT 59.933 44.000 0.00 0.00 0.00 3.41
3892 5308 2.416431 GGCTTGTTCATGATGGAACTGC 60.416 50.000 0.00 10.39 45.74 4.40
3959 5375 3.724478 ACTACAGATTCCAGGTCCATCA 58.276 45.455 0.00 0.00 0.00 3.07
3974 5390 5.109210 TCAAATATGCCAGACGAACTACAG 58.891 41.667 0.00 0.00 0.00 2.74
3987 5403 3.633525 TGAGCACTGGAATCAAATATGCC 59.366 43.478 0.00 0.00 31.94 4.40
4034 5450 9.906660 TTACCTTGTTAATTCATGTTGTGATTC 57.093 29.630 0.00 0.00 36.54 2.52
4085 5501 4.946772 TCACAATGTTTCCTCACAACAGAA 59.053 37.500 0.00 0.00 37.55 3.02
4086 5502 4.522114 TCACAATGTTTCCTCACAACAGA 58.478 39.130 0.00 0.00 37.55 3.41
4087 5503 4.576053 TCTCACAATGTTTCCTCACAACAG 59.424 41.667 0.00 0.00 37.55 3.16
4088 5504 4.522114 TCTCACAATGTTTCCTCACAACA 58.478 39.130 0.00 0.00 38.49 3.33
4089 5505 5.009010 ACATCTCACAATGTTTCCTCACAAC 59.991 40.000 0.00 0.00 36.47 3.32
4090 5506 5.132502 ACATCTCACAATGTTTCCTCACAA 58.867 37.500 0.00 0.00 36.47 3.33
4091 5507 4.717877 ACATCTCACAATGTTTCCTCACA 58.282 39.130 0.00 0.00 36.47 3.58
4092 5508 5.934625 ACTACATCTCACAATGTTTCCTCAC 59.065 40.000 0.00 0.00 40.32 3.51
4093 5509 5.934043 CACTACATCTCACAATGTTTCCTCA 59.066 40.000 0.00 0.00 40.32 3.86
4094 5510 5.934625 ACACTACATCTCACAATGTTTCCTC 59.065 40.000 0.00 0.00 40.32 3.71
4095 5511 5.869579 ACACTACATCTCACAATGTTTCCT 58.130 37.500 0.00 0.00 40.32 3.36
4096 5512 6.428159 AGAACACTACATCTCACAATGTTTCC 59.572 38.462 0.00 0.00 40.32 3.13
4097 5513 7.426929 AGAACACTACATCTCACAATGTTTC 57.573 36.000 0.00 0.00 40.32 2.78
4101 5543 8.385858 CACATAAGAACACTACATCTCACAATG 58.614 37.037 0.00 0.00 0.00 2.82
4126 5568 9.486123 TCCAAATTCTAACATTCCATATTTCCA 57.514 29.630 0.00 0.00 0.00 3.53
4459 5910 1.813513 AACAAAGCATCTGTCCGGAG 58.186 50.000 3.06 0.00 0.00 4.63
4477 5928 6.970043 GCAAACACGCCAGAATTATATTGTAA 59.030 34.615 0.00 0.00 0.00 2.41
4494 5945 0.370273 GCTCGGATACAGCAAACACG 59.630 55.000 0.00 0.00 39.54 4.49
4501 5952 3.438297 TTTCTACAGCTCGGATACAGC 57.562 47.619 0.00 0.00 39.89 4.40
4632 6115 7.112122 TCTTATATGAAATGCTGACAAGTGGT 58.888 34.615 0.00 0.00 0.00 4.16
4858 6345 4.141135 TGGACCACACTATTCTTTGGGAAA 60.141 41.667 0.00 0.00 37.49 3.13
4863 6350 4.389374 ACACTGGACCACACTATTCTTTG 58.611 43.478 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.