Multiple sequence alignment - TraesCS4B01G116400

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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 TraesCS4B01G116400 chr4B 100.000 4361 0 0 560 4920 134376583 134372223 0.000000e+00 8054.0
1 TraesCS4B01G116400 chr4B 86.325 117 14 2 1531 1646 648061780 648061895 5.170000e-25 126.0
2 TraesCS4B01G116400 chr4B 100.000 37 0 0 1 37 134377142 134377106 8.840000e-08 69.4
3 TraesCS4B01G116400 chr4D 94.243 4082 159 25 878 4920 94871915 94867871 0.000000e+00 6167.0
4 TraesCS4B01G116400 chr4D 82.492 297 31 6 563 850 94872197 94871913 1.770000e-59 241.0
5 TraesCS4B01G116400 chr4D 86.567 134 16 2 1531 1663 503140659 503140791 3.970000e-31 147.0
6 TraesCS4B01G116400 chr4A 95.618 3218 119 7 878 4074 485458723 485461939 0.000000e+00 5142.0
7 TraesCS4B01G116400 chr4A 91.971 137 7 2 4624 4756 485461943 485462079 6.500000e-44 189.0
8 TraesCS4B01G116400 chr4A 84.375 192 9 4 656 847 485458552 485458722 8.470000e-38 169.0
9 TraesCS4B01G116400 chr5A 93.855 179 10 1 1487 1664 570528226 570528048 8.120000e-68 268.0
10 TraesCS4B01G116400 chr5A 85.075 134 18 2 1531 1663 687366221 687366089 8.590000e-28 135.0
11 TraesCS4B01G116400 chr3D 84.874 119 15 3 1520 1637 530415857 530415973 3.110000e-22 117.0


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 TraesCS4B01G116400 chr4B 134372223 134377142 4919 True 4061.700000 8054 100.000000 1 4920 2 chr4B.!!$R1 4919
1 TraesCS4B01G116400 chr4D 94867871 94872197 4326 True 3204.000000 6167 88.367500 563 4920 2 chr4D.!!$R1 4357
2 TraesCS4B01G116400 chr4A 485458552 485462079 3527 False 1833.333333 5142 90.654667 656 4756 3 chr4A.!!$F1 4100

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
35 36 0.116541 AAGGGAGAAGAAGGGTCGGA 59.883 55.0 0.00 0.0 0.00 4.55 F
709 718 0.251916 TCCGACCAATTGCACCCTAG 59.748 55.0 0.00 0.0 0.00 3.02 F
1091 1112 0.609662 TACCCACGTACCAGCTTTCC 59.390 55.0 0.00 0.0 0.00 3.13 F
1329 1350 0.664466 TCGAGCTCTGCTTCAACGTG 60.664 55.0 12.85 0.0 39.88 4.49 F
2079 2100 0.175302 AGAGAAGAGGCGAGCATGTG 59.825 55.0 0.00 0.0 0.00 3.21 F
3304 3349 0.321653 GACGGCAAGAAGTCCATGGT 60.322 55.0 12.58 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1704 0.800631 TCGTCGTCGTCATGTTAGCT 59.199 50.000 1.33 0.00 38.33 3.32 R
1830 1851 1.003355 CACCTTGTCCATCACGGCT 60.003 57.895 0.00 0.00 38.80 5.52 R
2057 2078 1.134877 CATGCTCGCCTCTTCTCTTGA 60.135 52.381 0.00 0.00 0.00 3.02 R
2326 2347 1.550065 CCACGATCGAGCTTGTAGTG 58.450 55.000 24.34 5.83 0.00 2.74 R
3730 3775 0.523335 GCTAAAACATGGCGGCTTCG 60.523 55.000 11.43 0.44 0.00 3.79 R
4870 4929 0.108709 CACAAAATGATGTGGCGGGG 60.109 55.000 3.73 0.00 45.47 5.73 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
23 24 2.991250 GCAGATGCAAAGTAAGGGAGA 58.009 47.619 0.00 0.00 41.59 3.71
24 25 3.347216 GCAGATGCAAAGTAAGGGAGAA 58.653 45.455 0.00 0.00 41.59 2.87
25 26 3.376546 GCAGATGCAAAGTAAGGGAGAAG 59.623 47.826 0.00 0.00 41.59 2.85
26 27 4.836825 CAGATGCAAAGTAAGGGAGAAGA 58.163 43.478 0.00 0.00 0.00 2.87
27 28 5.248640 CAGATGCAAAGTAAGGGAGAAGAA 58.751 41.667 0.00 0.00 0.00 2.52
28 29 5.353678 CAGATGCAAAGTAAGGGAGAAGAAG 59.646 44.000 0.00 0.00 0.00 2.85
29 30 4.021102 TGCAAAGTAAGGGAGAAGAAGG 57.979 45.455 0.00 0.00 0.00 3.46
30 31 3.244911 TGCAAAGTAAGGGAGAAGAAGGG 60.245 47.826 0.00 0.00 0.00 3.95
31 32 3.244946 GCAAAGTAAGGGAGAAGAAGGGT 60.245 47.826 0.00 0.00 0.00 4.34
32 33 4.580868 CAAAGTAAGGGAGAAGAAGGGTC 58.419 47.826 0.00 0.00 0.00 4.46
33 34 2.458620 AGTAAGGGAGAAGAAGGGTCG 58.541 52.381 0.00 0.00 0.00 4.79
34 35 1.481363 GTAAGGGAGAAGAAGGGTCGG 59.519 57.143 0.00 0.00 0.00 4.79
35 36 0.116541 AAGGGAGAAGAAGGGTCGGA 59.883 55.000 0.00 0.00 0.00 4.55
36 37 0.340208 AGGGAGAAGAAGGGTCGGAT 59.660 55.000 0.00 0.00 0.00 4.18
585 586 0.532573 AGACCAGCGTTCGATGACAT 59.467 50.000 11.94 0.00 0.00 3.06
593 594 2.284288 GCGTTCGATGACATAACACGTC 60.284 50.000 12.04 0.00 0.00 4.34
594 595 2.278094 CGTTCGATGACATAACACGTCC 59.722 50.000 0.00 0.00 32.15 4.79
601 602 4.265904 TGACATAACACGTCCAGACAAT 57.734 40.909 0.00 0.00 32.15 2.71
604 605 7.102847 TGACATAACACGTCCAGACAATATA 57.897 36.000 0.00 0.00 32.15 0.86
605 606 7.200455 TGACATAACACGTCCAGACAATATAG 58.800 38.462 0.00 0.00 32.15 1.31
610 611 1.611977 CGTCCAGACAATATAGCCCGA 59.388 52.381 0.00 0.00 0.00 5.14
612 613 3.654414 GTCCAGACAATATAGCCCGAAG 58.346 50.000 0.00 0.00 0.00 3.79
628 631 1.450025 GAAGGTAGGCGGTTTTGAGG 58.550 55.000 0.00 0.00 0.00 3.86
632 635 0.675837 GTAGGCGGTTTTGAGGGTCC 60.676 60.000 0.00 0.00 0.00 4.46
639 642 1.146485 TTTTGAGGGTCCGCGTTGA 59.854 52.632 4.92 0.00 0.00 3.18
647 650 1.741770 GTCCGCGTTGAAGATGCCT 60.742 57.895 4.92 0.00 36.93 4.75
650 653 1.083489 CCGCGTTGAAGATGCCTTAA 58.917 50.000 4.92 0.00 36.93 1.85
651 654 1.466950 CCGCGTTGAAGATGCCTTAAA 59.533 47.619 4.92 0.00 36.93 1.52
694 703 0.877071 GAACTACACGACACCTCCGA 59.123 55.000 0.00 0.00 0.00 4.55
709 718 0.251916 TCCGACCAATTGCACCCTAG 59.748 55.000 0.00 0.00 0.00 3.02
739 748 2.211250 AAAGCAGCAGATCACCACAT 57.789 45.000 0.00 0.00 0.00 3.21
740 749 2.211250 AAGCAGCAGATCACCACATT 57.789 45.000 0.00 0.00 0.00 2.71
741 750 2.211250 AGCAGCAGATCACCACATTT 57.789 45.000 0.00 0.00 0.00 2.32
742 751 2.522185 AGCAGCAGATCACCACATTTT 58.478 42.857 0.00 0.00 0.00 1.82
743 752 2.490903 AGCAGCAGATCACCACATTTTC 59.509 45.455 0.00 0.00 0.00 2.29
744 753 2.416431 GCAGCAGATCACCACATTTTCC 60.416 50.000 0.00 0.00 0.00 3.13
745 754 2.086869 AGCAGATCACCACATTTTCCG 58.913 47.619 0.00 0.00 0.00 4.30
746 755 1.812571 GCAGATCACCACATTTTCCGT 59.187 47.619 0.00 0.00 0.00 4.69
747 756 2.228822 GCAGATCACCACATTTTCCGTT 59.771 45.455 0.00 0.00 0.00 4.44
748 757 3.305335 GCAGATCACCACATTTTCCGTTT 60.305 43.478 0.00 0.00 0.00 3.60
749 758 4.475944 CAGATCACCACATTTTCCGTTTC 58.524 43.478 0.00 0.00 0.00 2.78
750 759 3.506067 AGATCACCACATTTTCCGTTTCC 59.494 43.478 0.00 0.00 0.00 3.13
836 846 9.647797 AATTAGACATCTTAACACGTATGACAA 57.352 29.630 0.91 0.00 0.00 3.18
847 857 3.732219 CACGTATGACAACACTACAACGT 59.268 43.478 0.00 0.00 0.00 3.99
848 858 4.911033 CACGTATGACAACACTACAACGTA 59.089 41.667 0.00 0.00 0.00 3.57
849 859 4.911610 ACGTATGACAACACTACAACGTAC 59.088 41.667 0.00 0.00 0.00 3.67
850 860 4.911033 CGTATGACAACACTACAACGTACA 59.089 41.667 0.00 0.00 0.00 2.90
851 861 5.058856 CGTATGACAACACTACAACGTACAG 59.941 44.000 0.00 0.00 0.00 2.74
852 862 4.374843 TGACAACACTACAACGTACAGT 57.625 40.909 0.00 0.00 0.00 3.55
853 863 4.353737 TGACAACACTACAACGTACAGTC 58.646 43.478 0.00 0.00 0.00 3.51
854 864 4.142425 TGACAACACTACAACGTACAGTCA 60.142 41.667 0.00 0.00 0.00 3.41
855 865 4.107622 ACAACACTACAACGTACAGTCAC 58.892 43.478 0.00 0.00 0.00 3.67
856 866 3.360249 ACACTACAACGTACAGTCACC 57.640 47.619 0.00 0.00 0.00 4.02
857 867 2.035066 ACACTACAACGTACAGTCACCC 59.965 50.000 0.00 0.00 0.00 4.61
858 868 1.615392 ACTACAACGTACAGTCACCCC 59.385 52.381 0.00 0.00 0.00 4.95
859 869 1.891150 CTACAACGTACAGTCACCCCT 59.109 52.381 0.00 0.00 0.00 4.79
860 870 0.677842 ACAACGTACAGTCACCCCTC 59.322 55.000 0.00 0.00 0.00 4.30
861 871 0.677288 CAACGTACAGTCACCCCTCA 59.323 55.000 0.00 0.00 0.00 3.86
862 872 1.069513 CAACGTACAGTCACCCCTCAA 59.930 52.381 0.00 0.00 0.00 3.02
863 873 1.416243 ACGTACAGTCACCCCTCAAA 58.584 50.000 0.00 0.00 0.00 2.69
864 874 1.764134 ACGTACAGTCACCCCTCAAAA 59.236 47.619 0.00 0.00 0.00 2.44
865 875 2.171027 ACGTACAGTCACCCCTCAAAAA 59.829 45.455 0.00 0.00 0.00 1.94
1022 1038 3.449018 ACTCCATGCCACTTACTAGTCTG 59.551 47.826 0.00 0.00 30.26 3.51
1051 1067 2.682856 CAAGAAGAGAGAGCGAGCTAGT 59.317 50.000 0.00 0.00 0.00 2.57
1075 1094 2.547826 GCCAGGTAGATTCAACGTACC 58.452 52.381 0.00 0.00 37.13 3.34
1091 1112 0.609662 TACCCACGTACCAGCTTTCC 59.390 55.000 0.00 0.00 0.00 3.13
1215 1236 3.402681 CAGGTCACCCCGCTCCAT 61.403 66.667 0.00 0.00 38.74 3.41
1329 1350 0.664466 TCGAGCTCTGCTTCAACGTG 60.664 55.000 12.85 0.00 39.88 4.49
1353 1374 4.658786 AACCGCCTCCCCACCTCT 62.659 66.667 0.00 0.00 0.00 3.69
1401 1422 1.587568 GCACATGCAGCACCATCAA 59.412 52.632 0.00 0.00 41.59 2.57
1461 1482 3.399770 CTCGTCGCCGCGTTCAAA 61.400 61.111 13.39 0.00 0.00 2.69
1666 1687 3.117171 CCGTCTCCTCGTCGTCGT 61.117 66.667 1.33 0.00 38.33 4.34
1857 1878 1.131638 TGGACAAGGTGAGCAAGTCT 58.868 50.000 6.48 0.00 0.00 3.24
1923 1944 3.432588 CCGCTCTCCGTCACGTCT 61.433 66.667 0.00 0.00 34.38 4.18
1953 1974 2.367512 GCCAGGGAGGAGGTGGAT 60.368 66.667 0.00 0.00 41.22 3.41
1972 1993 4.069232 CCAAGACCGGCGAGCTCA 62.069 66.667 15.40 0.00 0.00 4.26
2043 2064 2.955022 TAGAGGACCTCGCCTACGCC 62.955 65.000 15.97 0.00 38.73 5.68
2079 2100 0.175302 AGAGAAGAGGCGAGCATGTG 59.825 55.000 0.00 0.00 0.00 3.21
2137 2158 1.153549 GCCGTCATGGAGGTGAGTC 60.154 63.158 8.73 0.00 42.00 3.36
2356 2385 0.930742 CGATCGTGGCTACTTCGAGC 60.931 60.000 14.42 2.20 42.05 5.03
2374 2416 3.060473 CGAGCCTCCGATCGTTAATTTTC 60.060 47.826 15.09 2.25 34.30 2.29
2487 2532 2.197324 GGTGGCCCTTGGTCAACA 59.803 61.111 0.00 0.00 45.59 3.33
2558 2603 2.727392 CCCGGAGCCGAACATACCA 61.727 63.158 11.05 0.00 42.83 3.25
2659 2704 5.593183 TGCATGCACAAAATTAACATGTG 57.407 34.783 18.46 11.00 45.54 3.21
2694 2739 0.384309 TTACTAGCATGGCGACGGAG 59.616 55.000 0.00 0.00 0.00 4.63
2867 2912 2.615493 CCTCTCCGGCTACAACAACAAT 60.615 50.000 0.00 0.00 0.00 2.71
2993 3038 0.741221 GTGATCTTCCTCGGTGGCAC 60.741 60.000 9.70 9.70 35.26 5.01
3032 3077 2.283298 CCAGAATCCATCACGGTTCAG 58.717 52.381 0.00 0.00 35.57 3.02
3042 3087 3.417069 TCACGGTTCAGTCCAATTCAT 57.583 42.857 0.00 0.00 0.00 2.57
3135 3180 1.640069 CTCAAGATCATGTGCGGCG 59.360 57.895 0.51 0.51 0.00 6.46
3278 3323 0.326264 GGCTGCTCTTCAAAGGGAGA 59.674 55.000 0.00 0.00 0.00 3.71
3304 3349 0.321653 GACGGCAAGAAGTCCATGGT 60.322 55.000 12.58 0.00 0.00 3.55
3312 3357 1.280421 AGAAGTCCATGGTTCTGGAGC 59.720 52.381 15.05 5.77 45.87 4.70
3332 3377 2.680913 CGCCAAGCTCGTCTTTGGG 61.681 63.158 13.55 5.70 31.27 4.12
3336 3381 0.955919 CAAGCTCGTCTTTGGGTCCC 60.956 60.000 0.00 0.00 31.27 4.46
3349 3394 1.202879 TGGGTCCCACAATGACTTCAC 60.203 52.381 6.47 0.00 33.22 3.18
3356 3401 3.012518 CCACAATGACTTCACCTCCATC 58.987 50.000 0.00 0.00 0.00 3.51
3473 3518 4.533222 CACAAAGGTTTTACGAAGCGATT 58.467 39.130 0.00 0.00 0.00 3.34
3730 3775 2.663196 CGTGGAGAAGGGGGTGAC 59.337 66.667 0.00 0.00 0.00 3.67
3771 3816 1.134694 GATTTGAACGAGTGCGCCC 59.865 57.895 4.18 0.00 42.48 6.13
3863 3908 4.829064 TGGTGTTTTCTTCTTCCGATTG 57.171 40.909 0.00 0.00 0.00 2.67
3903 3948 8.186163 CACATTAGCTTGCTTTTCATCATCTTA 58.814 33.333 0.00 0.00 0.00 2.10
3912 3957 8.746922 TGCTTTTCATCATCTTATCAACAAAC 57.253 30.769 0.00 0.00 0.00 2.93
3939 3984 1.187087 CCTAGACCTCAGAGCCGTTT 58.813 55.000 0.00 0.00 0.00 3.60
3940 3985 1.550976 CCTAGACCTCAGAGCCGTTTT 59.449 52.381 0.00 0.00 0.00 2.43
3941 3986 2.028020 CCTAGACCTCAGAGCCGTTTTT 60.028 50.000 0.00 0.00 0.00 1.94
4063 4108 3.314635 GTCTTTCATTATGGCTCTGGCAG 59.685 47.826 8.58 8.58 42.43 4.85
4065 4110 4.164030 TCTTTCATTATGGCTCTGGCAGTA 59.836 41.667 15.27 0.27 42.43 2.74
4074 4119 3.198872 GGCTCTGGCAGTAGTACAATTC 58.801 50.000 15.27 0.00 40.87 2.17
4075 4120 3.369471 GGCTCTGGCAGTAGTACAATTCA 60.369 47.826 15.27 0.00 40.87 2.57
4076 4121 4.446371 GCTCTGGCAGTAGTACAATTCAT 58.554 43.478 15.27 0.00 38.54 2.57
4078 4123 5.355350 GCTCTGGCAGTAGTACAATTCATTT 59.645 40.000 15.27 0.00 38.54 2.32
4079 4124 6.538742 GCTCTGGCAGTAGTACAATTCATTTA 59.461 38.462 15.27 0.00 38.54 1.40
4121 4168 9.064706 CATCCAATTAGAAGCAAGTGAGATATT 57.935 33.333 0.00 0.00 0.00 1.28
4161 4208 1.081892 CTGAGATCCTGTTGTTGCCG 58.918 55.000 0.00 0.00 0.00 5.69
4172 4219 2.223456 TGTTGTTGCCGTGTTGAATCTG 60.223 45.455 0.00 0.00 0.00 2.90
4177 4224 1.514678 GCCGTGTTGAATCTGGTGCA 61.515 55.000 0.00 0.00 0.00 4.57
4199 4246 2.422479 TCTACTTCTCGTTGGTCATCGG 59.578 50.000 2.26 0.00 0.00 4.18
4200 4247 0.389948 ACTTCTCGTTGGTCATCGGC 60.390 55.000 2.26 0.00 0.00 5.54
4201 4248 0.108615 CTTCTCGTTGGTCATCGGCT 60.109 55.000 2.26 0.00 0.00 5.52
4202 4249 0.108804 TTCTCGTTGGTCATCGGCTC 60.109 55.000 2.26 0.00 0.00 4.70
4203 4250 1.215382 CTCGTTGGTCATCGGCTCA 59.785 57.895 2.26 0.00 0.00 4.26
4204 4251 0.179100 CTCGTTGGTCATCGGCTCAT 60.179 55.000 2.26 0.00 0.00 2.90
4205 4252 0.179111 TCGTTGGTCATCGGCTCATC 60.179 55.000 2.26 0.00 0.00 2.92
4206 4253 1.482621 CGTTGGTCATCGGCTCATCG 61.483 60.000 0.00 0.00 0.00 3.84
4207 4254 1.521457 TTGGTCATCGGCTCATCGC 60.521 57.895 0.00 0.00 38.13 4.58
4228 4275 1.524621 CCGATGATGGAGTGTGCCC 60.525 63.158 0.00 0.00 0.00 5.36
4239 4289 1.001760 GTGTGCCCTCCTCCCTCTA 59.998 63.158 0.00 0.00 0.00 2.43
4273 4323 2.140792 CCCCCATGGTCCTCCTACG 61.141 68.421 11.73 0.00 34.23 3.51
4274 4324 2.140792 CCCCATGGTCCTCCTACGG 61.141 68.421 11.73 0.00 34.23 4.02
4276 4326 2.808206 CCATGGTCCTCCTACGGCC 61.808 68.421 2.57 0.00 34.23 6.13
4277 4327 1.762460 CATGGTCCTCCTACGGCCT 60.762 63.158 0.00 0.00 34.23 5.19
4278 4328 1.003051 ATGGTCCTCCTACGGCCTT 59.997 57.895 0.00 0.00 34.23 4.35
4374 4428 1.269723 GGTTTGTTCAAGGCTAGTGGC 59.730 52.381 0.00 0.00 40.90 5.01
4403 4457 1.171549 TTTGCGATGCTTGTGCTCCA 61.172 50.000 0.00 0.00 40.48 3.86
4404 4458 0.961857 TTGCGATGCTTGTGCTCCAT 60.962 50.000 0.00 0.00 40.48 3.41
4411 4465 1.242076 GCTTGTGCTCCATTCACAGT 58.758 50.000 0.00 0.00 44.18 3.55
4422 4476 2.095853 CCATTCACAGTAACATGTCGCC 59.904 50.000 0.00 0.00 0.00 5.54
4446 4500 2.461300 TGGTGGTCAAATTTGGGTCA 57.539 45.000 17.90 10.76 0.00 4.02
4448 4502 2.632028 TGGTGGTCAAATTTGGGTCATG 59.368 45.455 17.90 0.00 0.00 3.07
4485 4539 4.320494 GCTACAAGTTCTTGTTGTGGATGG 60.320 45.833 20.66 1.02 38.33 3.51
4489 4543 3.897239 AGTTCTTGTTGTGGATGGTTCA 58.103 40.909 0.00 0.00 0.00 3.18
4515 4569 2.168521 TCCATGCTAGTCTAGGTTGTGC 59.831 50.000 8.97 0.00 0.00 4.57
4518 4572 3.251479 TGCTAGTCTAGGTTGTGCATG 57.749 47.619 8.97 0.00 0.00 4.06
4527 4581 5.587844 GTCTAGGTTGTGCATGATCATCTTT 59.412 40.000 4.86 0.00 0.00 2.52
4528 4582 6.094603 GTCTAGGTTGTGCATGATCATCTTTT 59.905 38.462 4.86 0.00 0.00 2.27
4540 4594 6.220726 TGATCATCTTTTACTCGTGGATCA 57.779 37.500 0.00 0.00 37.98 2.92
4541 4595 6.276091 TGATCATCTTTTACTCGTGGATCAG 58.724 40.000 0.00 0.00 36.08 2.90
4549 4603 1.272781 CTCGTGGATCAGCGACTTTC 58.727 55.000 6.74 0.00 33.33 2.62
4574 4628 5.303845 GGGTTACTGATCCTAGGTCGTTTAT 59.696 44.000 9.08 0.00 0.00 1.40
4595 4649 5.931441 ATGTTTTCTCAGTTGAGTAGTGC 57.069 39.130 8.85 0.00 42.60 4.40
4596 4650 4.127171 TGTTTTCTCAGTTGAGTAGTGCC 58.873 43.478 8.85 0.00 42.60 5.01
4629 4683 2.751806 GTCTGCCTCATTCCTTCTTTGG 59.248 50.000 0.00 0.00 0.00 3.28
4636 4690 4.261741 CCTCATTCCTTCTTTGGTGTTGTG 60.262 45.833 0.00 0.00 0.00 3.33
4637 4691 3.068024 TCATTCCTTCTTTGGTGTTGTGC 59.932 43.478 0.00 0.00 0.00 4.57
4659 4713 8.587608 TGTGCCATCTTCTTTCTCAATAAATTT 58.412 29.630 0.00 0.00 0.00 1.82
4727 4781 7.411486 TTTTCCTGGTTCTGTCAAAATGTTA 57.589 32.000 0.00 0.00 0.00 2.41
4734 4788 6.829298 TGGTTCTGTCAAAATGTTACCTACAA 59.171 34.615 0.00 0.00 40.89 2.41
4777 4835 7.730364 ATCATTCTAAATACCGGACAACATC 57.270 36.000 9.46 0.00 0.00 3.06
4778 4836 6.645306 TCATTCTAAATACCGGACAACATCA 58.355 36.000 9.46 0.00 0.00 3.07
4782 4840 7.931578 TCTAAATACCGGACAACATCATTTT 57.068 32.000 9.46 0.00 0.00 1.82
4783 4841 8.343168 TCTAAATACCGGACAACATCATTTTT 57.657 30.769 9.46 0.00 0.00 1.94
4873 4932 8.683615 CCACTAAAATAACTCACTTAAATCCCC 58.316 37.037 0.00 0.00 0.00 4.81
4891 4950 1.402720 CCCGCCACATCATTTTGTGTC 60.403 52.381 4.12 0.00 44.42 3.67
4912 4971 5.717178 TGTCTGGCTCTTGACTAAGATAGTT 59.283 40.000 0.00 0.00 41.83 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.991250 TCTCCCTTACTTTGCATCTGC 58.009 47.619 0.00 0.00 42.50 4.26
4 5 4.836825 TCTTCTCCCTTACTTTGCATCTG 58.163 43.478 0.00 0.00 0.00 2.90
5 6 5.495640 CTTCTTCTCCCTTACTTTGCATCT 58.504 41.667 0.00 0.00 0.00 2.90
6 7 4.637977 CCTTCTTCTCCCTTACTTTGCATC 59.362 45.833 0.00 0.00 0.00 3.91
7 8 4.568592 CCCTTCTTCTCCCTTACTTTGCAT 60.569 45.833 0.00 0.00 0.00 3.96
8 9 3.244911 CCCTTCTTCTCCCTTACTTTGCA 60.245 47.826 0.00 0.00 0.00 4.08
9 10 3.244946 ACCCTTCTTCTCCCTTACTTTGC 60.245 47.826 0.00 0.00 0.00 3.68
10 11 4.580868 GACCCTTCTTCTCCCTTACTTTG 58.419 47.826 0.00 0.00 0.00 2.77
11 12 3.261137 CGACCCTTCTTCTCCCTTACTTT 59.739 47.826 0.00 0.00 0.00 2.66
12 13 2.832733 CGACCCTTCTTCTCCCTTACTT 59.167 50.000 0.00 0.00 0.00 2.24
13 14 2.458620 CGACCCTTCTTCTCCCTTACT 58.541 52.381 0.00 0.00 0.00 2.24
14 15 1.481363 CCGACCCTTCTTCTCCCTTAC 59.519 57.143 0.00 0.00 0.00 2.34
15 16 1.360162 TCCGACCCTTCTTCTCCCTTA 59.640 52.381 0.00 0.00 0.00 2.69
16 17 0.116541 TCCGACCCTTCTTCTCCCTT 59.883 55.000 0.00 0.00 0.00 3.95
17 18 0.340208 ATCCGACCCTTCTTCTCCCT 59.660 55.000 0.00 0.00 0.00 4.20
18 19 2.917804 ATCCGACCCTTCTTCTCCC 58.082 57.895 0.00 0.00 0.00 4.30
559 560 3.898517 TCGAACGCTGGTCTATATCAG 57.101 47.619 0.00 0.00 36.87 2.90
560 561 3.818773 TCATCGAACGCTGGTCTATATCA 59.181 43.478 0.00 0.00 0.00 2.15
561 562 4.159857 GTCATCGAACGCTGGTCTATATC 58.840 47.826 0.00 0.00 0.00 1.63
568 569 2.268298 GTTATGTCATCGAACGCTGGT 58.732 47.619 0.00 0.00 0.00 4.00
571 572 1.917955 CGTGTTATGTCATCGAACGCT 59.082 47.619 9.32 0.00 32.64 5.07
573 574 2.278094 GGACGTGTTATGTCATCGAACG 59.722 50.000 0.00 10.75 35.87 3.95
577 578 2.852413 GTCTGGACGTGTTATGTCATCG 59.148 50.000 0.00 0.00 35.87 3.84
585 586 4.202182 GGGCTATATTGTCTGGACGTGTTA 60.202 45.833 0.00 0.00 0.00 2.41
593 594 2.368875 ACCTTCGGGCTATATTGTCTGG 59.631 50.000 0.00 0.00 39.10 3.86
594 595 3.753294 ACCTTCGGGCTATATTGTCTG 57.247 47.619 0.00 0.00 39.10 3.51
601 602 0.896940 CCGCCTACCTTCGGGCTATA 60.897 60.000 0.00 0.00 45.57 1.31
610 611 0.037734 CCCTCAAAACCGCCTACCTT 59.962 55.000 0.00 0.00 0.00 3.50
612 613 0.675837 GACCCTCAAAACCGCCTACC 60.676 60.000 0.00 0.00 0.00 3.18
616 617 3.053896 CGGACCCTCAAAACCGCC 61.054 66.667 0.00 0.00 38.98 6.13
621 622 0.464013 TTCAACGCGGACCCTCAAAA 60.464 50.000 12.47 0.00 0.00 2.44
625 628 1.084370 CATCTTCAACGCGGACCCTC 61.084 60.000 12.47 0.00 0.00 4.30
628 631 2.750888 GGCATCTTCAACGCGGACC 61.751 63.158 12.47 0.00 0.00 4.46
632 635 2.505866 GTTTAAGGCATCTTCAACGCG 58.494 47.619 3.53 3.53 34.59 6.01
634 637 2.159572 CGGGTTTAAGGCATCTTCAACG 60.160 50.000 0.00 0.00 37.75 4.10
639 642 2.215942 AAGCGGGTTTAAGGCATCTT 57.784 45.000 0.00 0.00 37.03 2.40
647 650 2.288518 GGAATGTGCAAAGCGGGTTTAA 60.289 45.455 4.68 0.00 0.00 1.52
650 653 0.827507 AGGAATGTGCAAAGCGGGTT 60.828 50.000 0.00 0.00 0.00 4.11
651 654 0.827507 AAGGAATGTGCAAAGCGGGT 60.828 50.000 0.00 0.00 0.00 5.28
694 703 0.323725 CAGCCTAGGGTGCAATTGGT 60.324 55.000 27.07 0.00 36.81 3.67
727 736 4.475944 GAAACGGAAAATGTGGTGATCTG 58.524 43.478 0.00 0.00 0.00 2.90
739 748 3.771798 CGTTGGAAAAGGAAACGGAAAA 58.228 40.909 0.00 0.00 42.15 2.29
740 749 2.479901 GCGTTGGAAAAGGAAACGGAAA 60.480 45.455 8.95 0.00 45.08 3.13
741 750 1.065851 GCGTTGGAAAAGGAAACGGAA 59.934 47.619 8.95 0.00 45.08 4.30
742 751 0.664224 GCGTTGGAAAAGGAAACGGA 59.336 50.000 8.95 0.00 45.08 4.69
743 752 0.659123 CGCGTTGGAAAAGGAAACGG 60.659 55.000 0.00 0.00 45.08 4.44
745 754 0.248702 TGCGCGTTGGAAAAGGAAAC 60.249 50.000 8.43 0.00 0.00 2.78
746 755 0.248702 GTGCGCGTTGGAAAAGGAAA 60.249 50.000 8.43 0.00 0.00 3.13
747 756 1.357334 GTGCGCGTTGGAAAAGGAA 59.643 52.632 8.43 0.00 0.00 3.36
748 757 1.377366 TTGTGCGCGTTGGAAAAGGA 61.377 50.000 8.43 0.00 0.00 3.36
749 758 0.934436 CTTGTGCGCGTTGGAAAAGG 60.934 55.000 8.43 0.00 29.94 3.11
750 759 0.028770 TCTTGTGCGCGTTGGAAAAG 59.971 50.000 8.43 3.99 34.68 2.27
836 846 2.035066 GGGTGACTGTACGTTGTAGTGT 59.965 50.000 0.00 0.00 0.00 3.55
866 876 4.571984 GTCCCTGTACGTTGTAGTGTTTTT 59.428 41.667 0.00 0.00 0.00 1.94
867 877 4.122046 GTCCCTGTACGTTGTAGTGTTTT 58.878 43.478 0.00 0.00 0.00 2.43
868 878 3.132646 TGTCCCTGTACGTTGTAGTGTTT 59.867 43.478 0.00 0.00 0.00 2.83
869 879 2.694628 TGTCCCTGTACGTTGTAGTGTT 59.305 45.455 0.00 0.00 0.00 3.32
870 880 2.309613 TGTCCCTGTACGTTGTAGTGT 58.690 47.619 0.00 0.00 0.00 3.55
871 881 3.374220 TTGTCCCTGTACGTTGTAGTG 57.626 47.619 0.00 0.00 0.00 2.74
872 882 5.244626 AGTTATTGTCCCTGTACGTTGTAGT 59.755 40.000 0.00 0.00 0.00 2.73
873 883 5.717119 AGTTATTGTCCCTGTACGTTGTAG 58.283 41.667 0.00 0.00 0.00 2.74
874 884 5.726980 AGTTATTGTCCCTGTACGTTGTA 57.273 39.130 0.00 0.00 0.00 2.41
875 885 4.612264 AGTTATTGTCCCTGTACGTTGT 57.388 40.909 0.00 0.00 0.00 3.32
876 886 5.927689 TGTAAGTTATTGTCCCTGTACGTTG 59.072 40.000 0.00 0.00 0.00 4.10
1022 1038 2.738321 GCTCTCTCTTCTTGTGCTAGCC 60.738 54.545 13.29 4.15 0.00 3.93
1051 1067 1.403647 CGTTGAATCTACCTGGCGTGA 60.404 52.381 0.00 0.00 0.00 4.35
1075 1094 1.298859 GCAGGAAAGCTGGTACGTGG 61.299 60.000 0.00 0.00 0.00 4.94
1504 1525 4.498520 CGCGGACGTCTGCTGGAT 62.499 66.667 38.36 0.00 45.75 3.41
1683 1704 0.800631 TCGTCGTCGTCATGTTAGCT 59.199 50.000 1.33 0.00 38.33 3.32
1781 1802 1.648467 GATGACCAAGCACCGCTTCC 61.648 60.000 0.00 0.00 46.77 3.46
1830 1851 1.003355 CACCTTGTCCATCACGGCT 60.003 57.895 0.00 0.00 38.80 5.52
1857 1878 3.555324 TGCCGGTGGTGAAGCTCA 61.555 61.111 1.90 0.00 0.00 4.26
1936 1957 2.367512 ATCCACCTCCTCCCTGGC 60.368 66.667 0.00 0.00 35.26 4.85
1938 1959 2.750657 GGCATCCACCTCCTCCCTG 61.751 68.421 0.00 0.00 0.00 4.45
1968 1989 4.783841 CAAACGAGCGCGCTGAGC 62.784 66.667 41.82 23.71 42.48 4.26
2057 2078 1.134877 CATGCTCGCCTCTTCTCTTGA 60.135 52.381 0.00 0.00 0.00 3.02
2079 2100 4.961511 TGTGACTGTCCGCCGTGC 62.962 66.667 5.17 0.00 0.00 5.34
2326 2347 1.550065 CCACGATCGAGCTTGTAGTG 58.450 55.000 24.34 5.83 0.00 2.74
2356 2385 5.959554 CGTAAGAAAATTAACGATCGGAGG 58.040 41.667 20.98 0.00 37.53 4.30
2641 2686 4.294232 CCGTCACATGTTAATTTTGTGCA 58.706 39.130 0.00 0.00 40.38 4.57
2867 2912 1.649267 CGAGCTCATCGTCATCGGA 59.351 57.895 15.40 0.00 46.62 4.55
3032 3077 2.161609 GTGACCGTTGGATGAATTGGAC 59.838 50.000 0.00 0.00 0.00 4.02
3312 3357 1.630244 CCAAAGACGAGCTTGGCGAG 61.630 60.000 5.79 0.00 36.80 5.03
3332 3377 2.427506 GAGGTGAAGTCATTGTGGGAC 58.572 52.381 0.00 0.00 35.50 4.46
3336 3381 3.937706 GAGATGGAGGTGAAGTCATTGTG 59.062 47.826 0.00 0.00 0.00 3.33
3349 3394 1.370437 CCGGCTGATGAGATGGAGG 59.630 63.158 0.00 0.00 0.00 4.30
3372 3417 3.192103 AACTGGAGTGAACCGGGGC 62.192 63.158 6.32 0.00 40.34 5.80
3515 3560 6.457934 CGATCTCTGATTCAAGGTTCATTTGG 60.458 42.308 0.00 0.00 0.00 3.28
3730 3775 0.523335 GCTAAAACATGGCGGCTTCG 60.523 55.000 11.43 0.44 0.00 3.79
3771 3816 0.541392 TGTCCTTCATCATCACCGGG 59.459 55.000 6.32 0.00 0.00 5.73
3863 3908 1.463674 AATGTGACAAATCTCCCGGC 58.536 50.000 0.00 0.00 0.00 6.13
3903 3948 9.668497 GAGGTCTAGGTTAATTAGTTTGTTGAT 57.332 33.333 0.00 0.00 0.00 2.57
3912 3957 5.278561 CGGCTCTGAGGTCTAGGTTAATTAG 60.279 48.000 6.83 0.00 0.00 1.73
4107 4154 8.897752 GGATAGTTTGAAAATATCTCACTTGCT 58.102 33.333 20.39 0.00 0.00 3.91
4121 4168 7.556635 TCTCAGACGATCTAGGATAGTTTGAAA 59.443 37.037 12.24 1.47 40.38 2.69
4161 4208 4.256920 AGTAGATGCACCAGATTCAACAC 58.743 43.478 0.00 0.00 0.00 3.32
4172 4219 2.271800 CCAACGAGAAGTAGATGCACC 58.728 52.381 0.00 0.00 0.00 5.01
4177 4224 3.066900 CCGATGACCAACGAGAAGTAGAT 59.933 47.826 1.22 0.00 0.00 1.98
4199 4246 3.928779 TCATCGGGGGCGATGAGC 61.929 66.667 3.52 0.00 46.46 4.26
4202 4249 2.359107 CCATCATCGGGGGCGATG 60.359 66.667 0.06 0.06 44.93 3.84
4203 4250 2.526624 TCCATCATCGGGGGCGAT 60.527 61.111 0.00 0.00 0.00 4.58
4204 4251 3.233980 CTCCATCATCGGGGGCGA 61.234 66.667 0.00 0.00 0.00 5.54
4205 4252 3.550431 ACTCCATCATCGGGGGCG 61.550 66.667 0.00 0.00 0.00 6.13
4206 4253 2.111878 CACTCCATCATCGGGGGC 59.888 66.667 0.00 0.00 0.00 5.80
4207 4254 1.146930 CACACTCCATCATCGGGGG 59.853 63.158 0.00 0.00 0.00 5.40
4228 4275 1.490574 CCACAACCTAGAGGGAGGAG 58.509 60.000 0.00 0.00 39.15 3.69
4239 4289 4.579127 GGTGAACAGCCACAACCT 57.421 55.556 0.00 0.00 38.74 3.50
4374 4428 5.454554 CACAAGCATCGCAAAGATAAATCTG 59.545 40.000 0.00 0.00 37.52 2.90
4403 4457 1.999735 CGGCGACATGTTACTGTGAAT 59.000 47.619 0.00 0.00 0.00 2.57
4404 4458 1.269883 ACGGCGACATGTTACTGTGAA 60.270 47.619 16.62 0.00 0.00 3.18
4411 4465 1.264557 CACCAAAACGGCGACATGTTA 59.735 47.619 16.62 0.00 39.03 2.41
4422 4476 2.869192 CCCAAATTTGACCACCAAAACG 59.131 45.455 19.86 0.00 46.64 3.60
4435 4489 5.012975 AGCCACATTAACATGACCCAAATTT 59.987 36.000 0.00 0.00 34.11 1.82
4446 4500 2.093181 TGTAGCCGAGCCACATTAACAT 60.093 45.455 0.00 0.00 0.00 2.71
4448 4502 2.018542 TGTAGCCGAGCCACATTAAC 57.981 50.000 0.00 0.00 0.00 2.01
4489 4543 5.367937 ACAACCTAGACTAGCATGGAATCAT 59.632 40.000 3.76 0.00 0.00 2.45
4515 4569 6.703165 TGATCCACGAGTAAAAGATGATCATG 59.297 38.462 14.30 0.00 34.18 3.07
4518 4572 5.176590 GCTGATCCACGAGTAAAAGATGATC 59.823 44.000 0.00 0.00 0.00 2.92
4527 4581 1.460504 AGTCGCTGATCCACGAGTAA 58.539 50.000 11.80 0.00 40.02 2.24
4528 4582 1.460504 AAGTCGCTGATCCACGAGTA 58.539 50.000 13.33 0.00 40.88 2.59
4540 4594 0.963962 TCAGTAACCCGAAAGTCGCT 59.036 50.000 0.00 0.00 38.82 4.93
4541 4595 1.925185 GATCAGTAACCCGAAAGTCGC 59.075 52.381 0.00 0.00 38.82 5.19
4549 4603 1.607628 CGACCTAGGATCAGTAACCCG 59.392 57.143 17.98 0.00 0.00 5.28
4574 4628 4.127171 GGCACTACTCAACTGAGAAAACA 58.873 43.478 13.61 0.00 44.74 2.83
4619 4673 1.341482 TGGCACAACACCAAAGAAGGA 60.341 47.619 0.00 0.00 33.12 3.36
4659 4713 5.420725 ACCATGAAGAAGTGCTACATGTA 57.579 39.130 5.25 5.25 37.29 2.29
4839 4897 9.574516 AAGTGAGTTATTTTAGTGGAAAGTCAT 57.425 29.630 0.00 0.00 33.44 3.06
4840 4898 8.974060 AAGTGAGTTATTTTAGTGGAAAGTCA 57.026 30.769 0.00 0.00 0.00 3.41
4851 4910 6.319405 GGCGGGGATTTAAGTGAGTTATTTTA 59.681 38.462 0.00 0.00 0.00 1.52
4863 4922 2.051334 TGATGTGGCGGGGATTTAAG 57.949 50.000 0.00 0.00 0.00 1.85
4870 4929 0.108709 CACAAAATGATGTGGCGGGG 60.109 55.000 3.73 0.00 45.47 5.73
4891 4950 6.402222 ACAAACTATCTTAGTCAAGAGCCAG 58.598 40.000 0.00 0.00 43.92 4.85


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

AutoCloner maintained by Alex Coulton.