Multiple sequence alignment - TraesCS1D01G391600

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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 TraesCS1D01G391600 chr1D 100.000 2911 0 0 1 2911 462199430 462202340 0.000000e+00 5376.0
1 TraesCS1D01G391600 chr1D 87.755 196 23 1 2341 2536 462201229 462201423 8.120000e-56 228.0
2 TraesCS1D01G391600 chr1D 87.755 196 23 1 1800 1994 462201770 462201965 8.120000e-56 228.0
3 TraesCS1D01G391600 chr1D 90.083 121 12 0 1873 1993 462287257 462287377 1.080000e-34 158.0
4 TraesCS1D01G391600 chr1B 93.080 2081 109 20 823 2898 636838022 636840072 0.000000e+00 3013.0
5 TraesCS1D01G391600 chr1B 85.337 416 47 10 21 432 636837392 636837797 4.490000e-113 418.0
6 TraesCS1D01G391600 chr1B 85.470 234 27 6 506 735 636837801 636838031 1.350000e-58 237.0
7 TraesCS1D01G391600 chr1B 84.834 211 30 2 2326 2536 636838977 636839185 8.170000e-51 211.0
8 TraesCS1D01G391600 chr1B 86.294 197 20 4 1800 1994 636839529 636839720 1.060000e-49 207.0
9 TraesCS1D01G391600 chr1B 87.195 164 20 1 1832 1994 637329286 637329449 4.950000e-43 185.0
10 TraesCS1D01G391600 chr1B 84.615 169 25 1 2372 2539 637329284 637329452 1.790000e-37 167.0
11 TraesCS1D01G391600 chr1B 90.541 74 7 0 1873 1946 637326317 637326390 6.640000e-17 99.0
12 TraesCS1D01G391600 chr1A 93.260 1988 95 11 930 2911 554061198 554063152 0.000000e+00 2892.0
13 TraesCS1D01G391600 chr1A 82.932 457 49 18 36 479 554060438 554060878 4.550000e-103 385.0
14 TraesCS1D01G391600 chr1A 84.921 252 29 7 505 752 554060831 554061077 2.240000e-61 246.0
15 TraesCS1D01G391600 chr1A 87.745 204 22 2 1794 1994 554062584 554062787 4.850000e-58 235.0
16 TraesCS1D01G391600 chr1A 86.700 203 24 2 2334 2536 554062046 554062245 3.780000e-54 222.0
17 TraesCS1D01G391600 chr7A 80.788 406 64 12 1107 1509 108809303 108808909 3.640000e-79 305.0
18 TraesCS1D01G391600 chrUn 80.303 396 62 15 1107 1498 74596104 74596487 4.750000e-73 285.0
19 TraesCS1D01G391600 chrUn 97.826 46 1 0 779 824 418950699 418950744 2.400000e-11 80.5
20 TraesCS1D01G391600 chr7D 86.800 250 32 1 1260 1509 104566987 104566739 7.940000e-71 278.0
21 TraesCS1D01G391600 chr7D 86.486 74 8 2 480 551 425733660 425733733 2.400000e-11 80.5
22 TraesCS1D01G391600 chr7D 92.308 39 3 0 787 825 191795601 191795563 4.050000e-04 56.5
23 TraesCS1D01G391600 chr7B 80.211 379 63 11 1260 1632 62687726 62687354 1.030000e-69 274.0
24 TraesCS1D01G391600 chr3B 86.250 240 31 2 1260 1498 632817480 632817718 2.880000e-65 259.0
25 TraesCS1D01G391600 chr3B 97.059 34 1 0 791 824 289627893 289627860 1.130000e-04 58.4
26 TraesCS1D01G391600 chr6D 78.378 407 67 20 1107 1498 431846326 431846726 8.060000e-61 244.0
27 TraesCS1D01G391600 chr6D 93.023 43 3 0 789 831 434443324 434443282 2.420000e-06 63.9
28 TraesCS1D01G391600 chr6B 78.141 398 71 13 1107 1498 651987354 651987741 3.750000e-59 239.0
29 TraesCS1D01G391600 chr6B 100.000 32 0 0 793 824 25088293 25088324 3.130000e-05 60.2
30 TraesCS1D01G391600 chr5D 90.323 62 5 1 781 841 461429772 461429711 2.400000e-11 80.5
31 TraesCS1D01G391600 chr4D 95.455 44 2 0 784 827 43150418 43150461 1.450000e-08 71.3
32 TraesCS1D01G391600 chr5A 86.667 60 6 2 492 551 689597150 689597207 6.730000e-07 65.8
33 TraesCS1D01G391600 chr2B 97.143 35 1 0 790 824 782186529 782186495 3.130000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G391600 chr1D 462199430 462202340 2910 False 1944.0 5376 91.836667 1 2911 3 chr1D.!!$F2 2910
1 TraesCS1D01G391600 chr1B 636837392 636840072 2680 False 817.2 3013 87.003000 21 2898 5 chr1B.!!$F1 2877
2 TraesCS1D01G391600 chr1A 554060438 554063152 2714 False 796.0 2892 87.111600 36 2911 5 chr1A.!!$F1 2875

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
777 793 1.000506 CCGTCCGTATTATGGGTCAGG 59.999 57.143 2.07 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2553 2.026822 AGGCTGTGAAGAATTGGTCGAT 60.027 45.455 0.0 0.0 0.0 3.59 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
62 63 1.003718 GGGAGCAGTGTTTAGGCGT 60.004 57.895 0.00 0.00 0.00 5.68
64 65 1.298859 GGAGCAGTGTTTAGGCGTGG 61.299 60.000 0.00 0.00 0.00 4.94
75 78 1.886886 TAGGCGTGGGTTGTTTTCTC 58.113 50.000 0.00 0.00 0.00 2.87
115 119 4.153411 TGGTTATCATCGGGGTTTTTGTT 58.847 39.130 0.00 0.00 0.00 2.83
118 122 2.074729 TCATCGGGGTTTTTGTTGGT 57.925 45.000 0.00 0.00 0.00 3.67
130 134 5.852229 GGTTTTTGTTGGTTTTTCGGTTTTC 59.148 36.000 0.00 0.00 0.00 2.29
177 185 6.639632 TGGTCTTCTCATTCTTTCCTTTTG 57.360 37.500 0.00 0.00 0.00 2.44
179 187 6.607198 TGGTCTTCTCATTCTTTCCTTTTGTT 59.393 34.615 0.00 0.00 0.00 2.83
219 228 6.200808 TCTTTCGGTTTATGTTTCGGTTTTC 58.799 36.000 0.00 0.00 0.00 2.29
222 231 6.857777 TCGGTTTATGTTTCGGTTTTCTTA 57.142 33.333 0.00 0.00 0.00 2.10
249 258 6.348786 GGTTTTCTACGTTCCTTACCCATTTC 60.349 42.308 0.00 0.00 0.00 2.17
256 265 4.874396 CGTTCCTTACCCATTTCCTAGTTC 59.126 45.833 0.00 0.00 0.00 3.01
275 284 6.942532 AGTTCTTTTCAGCACATGTCTAAA 57.057 33.333 0.00 0.00 0.00 1.85
276 285 7.333528 AGTTCTTTTCAGCACATGTCTAAAA 57.666 32.000 0.00 0.05 0.00 1.52
277 286 7.771183 AGTTCTTTTCAGCACATGTCTAAAAA 58.229 30.769 0.00 1.21 0.00 1.94
300 310 7.862512 AAATTTCACACACATTGTCCATTTT 57.137 28.000 0.00 0.00 35.67 1.82
310 320 8.303156 CACACATTGTCCATTTTTCCTATACAA 58.697 33.333 0.00 0.00 0.00 2.41
349 359 9.745880 TTTATACACGTTTAGCATTTTCCAAAA 57.254 25.926 0.00 0.00 0.00 2.44
398 409 8.247562 TGTACGCTTTGATGCCTAATTTTTATT 58.752 29.630 0.00 0.00 0.00 1.40
437 448 9.655769 CATTTCTTGTATACATCTCAAAATCCG 57.344 33.333 6.36 0.00 0.00 4.18
438 449 9.613428 ATTTCTTGTATACATCTCAAAATCCGA 57.387 29.630 6.36 0.00 0.00 4.55
439 450 9.443323 TTTCTTGTATACATCTCAAAATCCGAA 57.557 29.630 6.36 0.00 0.00 4.30
440 451 9.443323 TTCTTGTATACATCTCAAAATCCGAAA 57.557 29.630 6.36 0.00 0.00 3.46
441 452 9.443323 TCTTGTATACATCTCAAAATCCGAAAA 57.557 29.630 6.36 0.00 0.00 2.29
442 453 9.490663 CTTGTATACATCTCAAAATCCGAAAAC 57.509 33.333 6.36 0.00 0.00 2.43
443 454 8.554835 TGTATACATCTCAAAATCCGAAAACA 57.445 30.769 0.08 0.00 0.00 2.83
444 455 9.173021 TGTATACATCTCAAAATCCGAAAACAT 57.827 29.630 0.08 0.00 0.00 2.71
445 456 9.438291 GTATACATCTCAAAATCCGAAAACATG 57.562 33.333 0.00 0.00 0.00 3.21
446 457 6.331369 ACATCTCAAAATCCGAAAACATGT 57.669 33.333 0.00 0.00 0.00 3.21
447 458 6.748132 ACATCTCAAAATCCGAAAACATGTT 58.252 32.000 4.92 4.92 0.00 2.71
448 459 7.209475 ACATCTCAAAATCCGAAAACATGTTT 58.791 30.769 18.13 18.13 0.00 2.83
449 460 8.356657 ACATCTCAAAATCCGAAAACATGTTTA 58.643 29.630 23.53 9.03 31.63 2.01
450 461 9.190858 CATCTCAAAATCCGAAAACATGTTTAA 57.809 29.630 23.53 10.49 31.63 1.52
451 462 8.568732 TCTCAAAATCCGAAAACATGTTTAAC 57.431 30.769 23.53 18.20 31.63 2.01
452 463 8.191446 TCTCAAAATCCGAAAACATGTTTAACA 58.809 29.630 23.53 9.07 31.63 2.41
453 464 8.879342 TCAAAATCCGAAAACATGTTTAACAT 57.121 26.923 23.53 8.58 39.91 2.71
454 465 9.319143 TCAAAATCCGAAAACATGTTTAACATT 57.681 25.926 23.53 15.40 36.53 2.71
455 466 9.928236 CAAAATCCGAAAACATGTTTAACATTT 57.072 25.926 23.53 19.34 36.53 2.32
505 516 9.941325 TCAAATGTATGTTTTGATGCCTAATTT 57.059 25.926 0.00 0.00 37.97 1.82
610 625 8.791355 AACATTTTCCAAATAGACGTTGTAAC 57.209 30.769 0.00 0.00 0.00 2.50
715 731 4.821805 GTCAAGACCATGTTTGGAGAGAAA 59.178 41.667 0.00 0.00 46.92 2.52
761 777 7.766219 TTTTAGACAAATATGCTACTCCGTC 57.234 36.000 0.00 0.00 0.00 4.79
762 778 4.323553 AGACAAATATGCTACTCCGTCC 57.676 45.455 0.00 0.00 0.00 4.79
763 779 3.050619 GACAAATATGCTACTCCGTCCG 58.949 50.000 0.00 0.00 0.00 4.79
764 780 2.429610 ACAAATATGCTACTCCGTCCGT 59.570 45.455 0.00 0.00 0.00 4.69
765 781 3.633525 ACAAATATGCTACTCCGTCCGTA 59.366 43.478 0.00 0.00 0.00 4.02
766 782 4.280174 ACAAATATGCTACTCCGTCCGTAT 59.720 41.667 0.00 0.00 0.00 3.06
767 783 5.221382 ACAAATATGCTACTCCGTCCGTATT 60.221 40.000 0.00 0.00 0.00 1.89
768 784 6.016024 ACAAATATGCTACTCCGTCCGTATTA 60.016 38.462 0.00 0.00 0.00 0.98
769 785 6.770746 AATATGCTACTCCGTCCGTATTAT 57.229 37.500 0.00 0.00 0.00 1.28
770 786 3.909776 TGCTACTCCGTCCGTATTATG 57.090 47.619 0.00 0.00 0.00 1.90
771 787 2.555325 TGCTACTCCGTCCGTATTATGG 59.445 50.000 0.00 0.00 0.00 2.74
772 788 2.094854 GCTACTCCGTCCGTATTATGGG 60.095 54.545 2.07 0.00 0.00 4.00
773 789 2.077687 ACTCCGTCCGTATTATGGGT 57.922 50.000 2.07 0.00 0.00 4.51
774 790 1.959282 ACTCCGTCCGTATTATGGGTC 59.041 52.381 2.07 0.00 0.00 4.46
775 791 1.958579 CTCCGTCCGTATTATGGGTCA 59.041 52.381 2.07 0.00 0.00 4.02
776 792 1.958579 TCCGTCCGTATTATGGGTCAG 59.041 52.381 2.07 0.00 0.00 3.51
777 793 1.000506 CCGTCCGTATTATGGGTCAGG 59.999 57.143 2.07 0.00 0.00 3.86
778 794 1.958579 CGTCCGTATTATGGGTCAGGA 59.041 52.381 2.07 0.00 0.00 3.86
779 795 2.288030 CGTCCGTATTATGGGTCAGGAC 60.288 54.545 2.07 1.95 42.17 3.85
795 811 5.758924 GTCAGGACCACTAATGTCAAAAAC 58.241 41.667 0.00 0.00 34.36 2.43
796 812 4.513692 TCAGGACCACTAATGTCAAAAACG 59.486 41.667 0.00 0.00 34.36 3.60
797 813 3.252458 AGGACCACTAATGTCAAAAACGC 59.748 43.478 0.00 0.00 34.36 4.84
798 814 3.252458 GGACCACTAATGTCAAAAACGCT 59.748 43.478 0.00 0.00 34.36 5.07
799 815 4.464112 GACCACTAATGTCAAAAACGCTC 58.536 43.478 0.00 0.00 32.91 5.03
800 816 4.134563 ACCACTAATGTCAAAAACGCTCT 58.865 39.130 0.00 0.00 0.00 4.09
801 817 4.213482 ACCACTAATGTCAAAAACGCTCTC 59.787 41.667 0.00 0.00 0.00 3.20
802 818 4.213270 CCACTAATGTCAAAAACGCTCTCA 59.787 41.667 0.00 0.00 0.00 3.27
803 819 5.106555 CCACTAATGTCAAAAACGCTCTCAT 60.107 40.000 0.00 0.00 0.00 2.90
804 820 6.092122 CCACTAATGTCAAAAACGCTCTCATA 59.908 38.462 0.00 0.00 0.00 2.15
805 821 7.201644 CCACTAATGTCAAAAACGCTCTCATAT 60.202 37.037 0.00 0.00 0.00 1.78
806 822 8.177663 CACTAATGTCAAAAACGCTCTCATATT 58.822 33.333 0.00 0.00 0.00 1.28
807 823 9.378551 ACTAATGTCAAAAACGCTCTCATATTA 57.621 29.630 0.00 0.00 0.00 0.98
810 826 7.015226 TGTCAAAAACGCTCTCATATTATGG 57.985 36.000 3.89 0.00 0.00 2.74
811 827 6.038161 TGTCAAAAACGCTCTCATATTATGGG 59.962 38.462 3.89 0.31 0.00 4.00
812 828 6.260050 GTCAAAAACGCTCTCATATTATGGGA 59.740 38.462 6.10 6.10 37.45 4.37
813 829 6.260050 TCAAAAACGCTCTCATATTATGGGAC 59.740 38.462 1.94 0.28 34.11 4.46
814 830 3.577649 ACGCTCTCATATTATGGGACG 57.422 47.619 18.60 18.60 38.95 4.79
815 831 2.231478 ACGCTCTCATATTATGGGACGG 59.769 50.000 21.59 12.28 38.05 4.79
816 832 2.492088 CGCTCTCATATTATGGGACGGA 59.508 50.000 15.11 3.92 34.11 4.69
817 833 3.428180 CGCTCTCATATTATGGGACGGAG 60.428 52.174 15.11 10.86 34.11 4.63
818 834 3.118956 GCTCTCATATTATGGGACGGAGG 60.119 52.174 1.94 0.00 34.11 4.30
819 835 3.441101 TCTCATATTATGGGACGGAGGG 58.559 50.000 1.94 0.00 34.11 4.30
820 836 3.076937 TCTCATATTATGGGACGGAGGGA 59.923 47.826 1.94 0.00 34.11 4.20
821 837 3.441101 TCATATTATGGGACGGAGGGAG 58.559 50.000 3.89 0.00 0.00 4.30
826 842 4.474303 TTATGGGACGGAGGGAGTATAA 57.526 45.455 0.00 0.00 0.00 0.98
827 843 2.077687 TGGGACGGAGGGAGTATAAC 57.922 55.000 0.00 0.00 0.00 1.89
860 876 2.524394 ACACGGAGACAGGCTGGT 60.524 61.111 20.34 5.26 0.00 4.00
893 927 2.749800 GCCTTTTATCTACAGGCCCAGG 60.750 54.545 0.00 0.00 46.55 4.45
954 1000 3.806380 CTTCTGTGATGGGGATCTTGAG 58.194 50.000 0.00 0.00 0.00 3.02
1002 1048 1.909287 TGGACCGTCCAATCCACGA 60.909 57.895 18.34 0.00 45.00 4.35
1069 1115 2.692741 CACCTCCTCCCCCTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
1181 1227 1.542187 GGGCTACAAGAGGTGACCGT 61.542 60.000 0.00 0.00 0.00 4.83
1316 1362 3.011517 CCAGGTGGAGGGGGTGAG 61.012 72.222 0.00 0.00 37.39 3.51
1531 1578 2.325082 GCCTTCGCACACCATCGTT 61.325 57.895 0.00 0.00 34.03 3.85
1535 1582 1.593006 CTTCGCACACCATCGTTATCC 59.407 52.381 0.00 0.00 0.00 2.59
1556 1603 1.210931 CGTGCCCTTTGCTGATGTG 59.789 57.895 0.00 0.00 42.00 3.21
1558 1605 0.675633 GTGCCCTTTGCTGATGTGTT 59.324 50.000 0.00 0.00 42.00 3.32
1626 1673 0.620410 ATGTACCCCAGCAGCACCTA 60.620 55.000 0.00 0.00 0.00 3.08
1660 1707 6.341316 TGTGTCCTGATACTAATTCTTCAGC 58.659 40.000 0.00 0.00 35.38 4.26
1662 1709 5.127194 TGTCCTGATACTAATTCTTCAGCGT 59.873 40.000 0.00 0.00 35.38 5.07
1669 1716 8.414003 TGATACTAATTCTTCAGCGTCTTATGT 58.586 33.333 0.00 0.00 0.00 2.29
1670 1717 6.893958 ACTAATTCTTCAGCGTCTTATGTG 57.106 37.500 0.00 0.00 0.00 3.21
1685 1732 6.237728 CGTCTTATGTGCGTATAATGTGTGTT 60.238 38.462 0.00 0.00 0.00 3.32
1686 1733 7.461107 GTCTTATGTGCGTATAATGTGTGTTT 58.539 34.615 0.00 0.00 0.00 2.83
1687 1734 8.597227 GTCTTATGTGCGTATAATGTGTGTTTA 58.403 33.333 0.00 0.00 0.00 2.01
1688 1735 9.320352 TCTTATGTGCGTATAATGTGTGTTTAT 57.680 29.630 0.00 0.00 0.00 1.40
1689 1736 9.929722 CTTATGTGCGTATAATGTGTGTTTATT 57.070 29.630 0.00 0.00 0.00 1.40
1691 1738 8.835467 ATGTGCGTATAATGTGTGTTTATTTC 57.165 30.769 0.00 0.00 0.00 2.17
1692 1739 7.807680 TGTGCGTATAATGTGTGTTTATTTCA 58.192 30.769 0.00 0.00 0.00 2.69
1693 1740 7.960195 TGTGCGTATAATGTGTGTTTATTTCAG 59.040 33.333 0.00 0.00 0.00 3.02
1694 1741 7.960738 GTGCGTATAATGTGTGTTTATTTCAGT 59.039 33.333 0.00 0.00 0.00 3.41
1695 1742 7.960195 TGCGTATAATGTGTGTTTATTTCAGTG 59.040 33.333 0.00 0.00 0.00 3.66
1696 1743 8.172484 GCGTATAATGTGTGTTTATTTCAGTGA 58.828 33.333 0.00 0.00 0.00 3.41
1879 1943 4.473520 CTGCGGGGTGCTCGGAAT 62.474 66.667 0.00 0.00 46.63 3.01
1880 1944 4.467084 TGCGGGGTGCTCGGAATC 62.467 66.667 0.00 0.00 46.63 2.52
2021 2085 7.247456 TCATAACCCTTATAATCGTGGCATA 57.753 36.000 0.00 0.00 0.00 3.14
2041 2105 7.441157 TGGCATATAAAGTTAGCATGTAGTGAC 59.559 37.037 0.00 0.00 0.00 3.67
2049 2113 2.251818 AGCATGTAGTGACTGGTGAGT 58.748 47.619 0.00 0.00 33.98 3.41
2062 2126 3.181397 CTGGTGAGTTTTGTTTGCTGTG 58.819 45.455 0.00 0.00 0.00 3.66
2097 2161 6.992664 ACATTTCTAGCATCATCTACTCCT 57.007 37.500 0.00 0.00 0.00 3.69
2152 2216 4.895889 TGGTGATGTATTAGTCTCTGGAGG 59.104 45.833 0.00 0.00 0.00 4.30
2157 2221 6.207614 TGATGTATTAGTCTCTGGAGGATTCG 59.792 42.308 0.00 0.00 0.00 3.34
2173 2237 4.211374 AGGATTCGACTTGTCTTTGTTTCG 59.789 41.667 0.00 0.00 0.00 3.46
2182 2246 4.427096 TGTCTTTGTTTCGCTTGTGAAA 57.573 36.364 5.38 5.38 35.58 2.69
2183 2247 4.799678 TGTCTTTGTTTCGCTTGTGAAAA 58.200 34.783 10.39 0.78 39.40 2.29
2185 2249 5.866633 TGTCTTTGTTTCGCTTGTGAAAATT 59.133 32.000 10.39 0.00 39.40 1.82
2189 2253 5.820926 TGTTTCGCTTGTGAAAATTATGC 57.179 34.783 10.39 0.00 39.40 3.14
2193 2257 3.858812 TCGCTTGTGAAAATTATGCATGC 59.141 39.130 11.82 11.82 0.00 4.06
2238 2302 1.715931 TCCCCCATCAGTGTTTCCAAT 59.284 47.619 0.00 0.00 0.00 3.16
2288 2352 0.719465 GTTCACGCATAGTCAACCCG 59.281 55.000 0.00 0.00 0.00 5.28
2294 2358 1.860950 CGCATAGTCAACCCGAGAATG 59.139 52.381 0.00 0.00 0.00 2.67
2431 2496 3.330720 CTCGGAAGTTGGGGCCCT 61.331 66.667 25.93 1.90 0.00 5.19
2436 2501 1.271379 CGGAAGTTGGGGCCCTATATG 60.271 57.143 25.93 3.70 0.00 1.78
2443 2508 1.068121 GGGGCCCTATATGAAGTGCT 58.932 55.000 24.38 0.00 0.00 4.40
2478 2543 1.197721 CGAGGATGTGCTTTGGTTGAC 59.802 52.381 0.00 0.00 0.00 3.18
2488 2553 3.128349 GCTTTGGTTGACGAGTTACTCA 58.872 45.455 13.14 0.00 0.00 3.41
2566 2631 6.039382 TCGTTAGTGTATCACTCATGCAGTAT 59.961 38.462 5.66 0.00 41.21 2.12
2588 2653 4.793071 TGATTGATTTGCTTGTTGTACCG 58.207 39.130 0.00 0.00 0.00 4.02
2591 2656 4.640789 TGATTTGCTTGTTGTACCGTTT 57.359 36.364 0.00 0.00 0.00 3.60
2593 2658 4.800993 TGATTTGCTTGTTGTACCGTTTTG 59.199 37.500 0.00 0.00 0.00 2.44
2667 2732 7.857456 TGCATATGTTTCCCTTAAGTCTAGAA 58.143 34.615 4.29 0.00 0.00 2.10
2708 2773 2.883386 GAGCTAGATGGGCTTTTGGATG 59.117 50.000 0.00 0.00 40.40 3.51
2772 2838 7.582667 ATCTTTACTTGCTACCTGTGTTTTT 57.417 32.000 0.00 0.00 0.00 1.94
2778 2844 6.503524 ACTTGCTACCTGTGTTTTTATGTTG 58.496 36.000 0.00 0.00 0.00 3.33
2781 2847 5.010516 TGCTACCTGTGTTTTTATGTTGCAT 59.989 36.000 0.00 0.00 31.49 3.96
2788 2854 8.810427 CCTGTGTTTTTATGTTGCATTGATATC 58.190 33.333 0.00 0.00 0.00 1.63
2789 2855 9.356433 CTGTGTTTTTATGTTGCATTGATATCA 57.644 29.630 0.00 0.00 0.00 2.15
2790 2856 9.138062 TGTGTTTTTATGTTGCATTGATATCAC 57.862 29.630 4.48 0.00 0.00 3.06
2791 2857 9.357652 GTGTTTTTATGTTGCATTGATATCACT 57.642 29.630 4.48 0.00 0.00 3.41
2821 2887 7.736447 ATGTAGTCTCTTTTCCTGAAAGTTG 57.264 36.000 0.00 0.00 44.17 3.16
2898 2964 2.487372 GCTTCTCTTTCTCTTTGCAGGG 59.513 50.000 0.00 0.00 0.00 4.45
2900 2966 3.131709 TCTCTTTCTCTTTGCAGGGTG 57.868 47.619 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.821969 CCCACGCCTATATAACGTAGGT 59.178 50.000 11.75 0.00 40.69 3.08
1 2 2.821969 ACCCACGCCTATATAACGTAGG 59.178 50.000 15.98 15.98 43.01 3.18
2 3 4.022935 TCAACCCACGCCTATATAACGTAG 60.023 45.833 9.44 7.50 38.09 3.51
3 4 3.888323 TCAACCCACGCCTATATAACGTA 59.112 43.478 9.44 0.00 38.09 3.57
4 5 2.694628 TCAACCCACGCCTATATAACGT 59.305 45.455 4.98 4.98 41.45 3.99
5 6 3.054878 GTCAACCCACGCCTATATAACG 58.945 50.000 3.86 3.86 0.00 3.18
6 7 3.396560 GGTCAACCCACGCCTATATAAC 58.603 50.000 0.00 0.00 0.00 1.89
7 8 3.756933 GGTCAACCCACGCCTATATAA 57.243 47.619 0.00 0.00 0.00 0.98
53 54 2.359848 AGAAAACAACCCACGCCTAAAC 59.640 45.455 0.00 0.00 0.00 2.01
85 88 2.291465 CCCGATGATAACCAATGCAGTG 59.709 50.000 7.29 7.29 0.00 3.66
86 89 2.575532 CCCGATGATAACCAATGCAGT 58.424 47.619 0.00 0.00 0.00 4.40
88 91 1.214175 ACCCCGATGATAACCAATGCA 59.786 47.619 0.00 0.00 0.00 3.96
90 93 5.108517 CAAAAACCCCGATGATAACCAATG 58.891 41.667 0.00 0.00 0.00 2.82
91 94 4.775253 ACAAAAACCCCGATGATAACCAAT 59.225 37.500 0.00 0.00 0.00 3.16
98 101 2.604139 ACCAACAAAAACCCCGATGAT 58.396 42.857 0.00 0.00 0.00 2.45
115 119 1.817447 ACACCGAAAACCGAAAAACCA 59.183 42.857 0.00 0.00 41.76 3.67
118 122 4.437772 AGAAACACCGAAAACCGAAAAA 57.562 36.364 0.00 0.00 41.76 1.94
130 134 7.360946 CCAAAGATAACCTCTAAAGAAACACCG 60.361 40.741 0.00 0.00 32.41 4.94
177 185 8.865978 ACCGAAAGAAAAGAAATAAACAACAAC 58.134 29.630 0.00 0.00 0.00 3.32
179 187 8.989653 AACCGAAAGAAAAGAAATAAACAACA 57.010 26.923 0.00 0.00 0.00 3.33
206 214 7.722363 AGAAAACCATAAGAAAACCGAAACAT 58.278 30.769 0.00 0.00 0.00 2.71
207 215 7.102847 AGAAAACCATAAGAAAACCGAAACA 57.897 32.000 0.00 0.00 0.00 2.83
208 216 7.321984 CGTAGAAAACCATAAGAAAACCGAAAC 59.678 37.037 0.00 0.00 0.00 2.78
209 217 7.012232 ACGTAGAAAACCATAAGAAAACCGAAA 59.988 33.333 0.00 0.00 0.00 3.46
219 228 6.314648 GGGTAAGGAACGTAGAAAACCATAAG 59.685 42.308 10.36 0.00 0.00 1.73
222 231 4.041938 TGGGTAAGGAACGTAGAAAACCAT 59.958 41.667 10.36 0.00 0.00 3.55
249 258 4.999950 AGACATGTGCTGAAAAGAACTAGG 59.000 41.667 1.15 0.00 0.00 3.02
275 284 7.862512 AAATGGACAATGTGTGTGAAATTTT 57.137 28.000 0.00 0.00 41.96 1.82
276 285 7.862512 AAAATGGACAATGTGTGTGAAATTT 57.137 28.000 0.00 0.00 41.96 1.82
277 286 7.012232 GGAAAAATGGACAATGTGTGTGAAATT 59.988 33.333 0.00 0.00 41.96 1.82
278 287 6.482973 GGAAAAATGGACAATGTGTGTGAAAT 59.517 34.615 0.00 0.00 41.96 2.17
416 427 9.490663 GTTTTCGGATTTTGAGATGTATACAAG 57.509 33.333 10.14 0.00 0.00 3.16
755 771 1.958579 TGACCCATAATACGGACGGAG 59.041 52.381 0.00 0.00 0.00 4.63
756 772 1.958579 CTGACCCATAATACGGACGGA 59.041 52.381 0.00 0.00 0.00 4.69
757 773 1.000506 CCTGACCCATAATACGGACGG 59.999 57.143 0.00 0.00 0.00 4.79
758 774 1.958579 TCCTGACCCATAATACGGACG 59.041 52.381 0.00 0.00 0.00 4.79
759 775 2.036862 GGTCCTGACCCATAATACGGAC 59.963 54.545 4.93 0.00 45.68 4.79
760 776 2.322658 GGTCCTGACCCATAATACGGA 58.677 52.381 4.93 0.00 45.68 4.69
761 777 2.833631 GGTCCTGACCCATAATACGG 57.166 55.000 4.93 0.00 45.68 4.02
772 788 5.560183 CGTTTTTGACATTAGTGGTCCTGAC 60.560 44.000 0.00 0.00 34.36 3.51
773 789 4.513692 CGTTTTTGACATTAGTGGTCCTGA 59.486 41.667 0.00 0.00 34.36 3.86
774 790 4.783242 CGTTTTTGACATTAGTGGTCCTG 58.217 43.478 0.00 0.00 34.36 3.86
775 791 3.252458 GCGTTTTTGACATTAGTGGTCCT 59.748 43.478 0.00 0.00 34.36 3.85
776 792 3.252458 AGCGTTTTTGACATTAGTGGTCC 59.748 43.478 0.00 0.00 34.36 4.46
777 793 4.213482 AGAGCGTTTTTGACATTAGTGGTC 59.787 41.667 0.00 0.00 35.83 4.02
778 794 4.134563 AGAGCGTTTTTGACATTAGTGGT 58.865 39.130 0.00 0.00 0.00 4.16
779 795 4.213270 TGAGAGCGTTTTTGACATTAGTGG 59.787 41.667 0.00 0.00 0.00 4.00
780 796 5.342806 TGAGAGCGTTTTTGACATTAGTG 57.657 39.130 0.00 0.00 0.00 2.74
781 797 7.849804 ATATGAGAGCGTTTTTGACATTAGT 57.150 32.000 0.00 0.00 0.00 2.24
784 800 8.131100 CCATAATATGAGAGCGTTTTTGACATT 58.869 33.333 1.10 0.00 0.00 2.71
785 801 7.255242 CCCATAATATGAGAGCGTTTTTGACAT 60.255 37.037 1.10 0.00 0.00 3.06
786 802 6.038161 CCCATAATATGAGAGCGTTTTTGACA 59.962 38.462 1.10 0.00 0.00 3.58
787 803 6.260050 TCCCATAATATGAGAGCGTTTTTGAC 59.740 38.462 1.10 0.00 0.00 3.18
788 804 6.260050 GTCCCATAATATGAGAGCGTTTTTGA 59.740 38.462 1.10 0.00 0.00 2.69
789 805 6.430451 GTCCCATAATATGAGAGCGTTTTTG 58.570 40.000 1.10 0.00 0.00 2.44
790 806 5.236478 CGTCCCATAATATGAGAGCGTTTTT 59.764 40.000 1.10 0.00 0.00 1.94
791 807 4.750098 CGTCCCATAATATGAGAGCGTTTT 59.250 41.667 1.10 0.00 0.00 2.43
792 808 4.307432 CGTCCCATAATATGAGAGCGTTT 58.693 43.478 1.10 0.00 0.00 3.60
793 809 3.306088 CCGTCCCATAATATGAGAGCGTT 60.306 47.826 1.10 0.00 0.00 4.84
794 810 2.231478 CCGTCCCATAATATGAGAGCGT 59.769 50.000 1.10 0.00 0.00 5.07
795 811 2.492088 TCCGTCCCATAATATGAGAGCG 59.508 50.000 1.10 1.62 0.00 5.03
796 812 3.118956 CCTCCGTCCCATAATATGAGAGC 60.119 52.174 1.10 0.00 0.00 4.09
797 813 3.449018 CCCTCCGTCCCATAATATGAGAG 59.551 52.174 1.10 0.73 0.00 3.20
798 814 3.076937 TCCCTCCGTCCCATAATATGAGA 59.923 47.826 1.10 0.00 0.00 3.27
799 815 3.441101 TCCCTCCGTCCCATAATATGAG 58.559 50.000 1.10 0.00 0.00 2.90
800 816 3.181410 ACTCCCTCCGTCCCATAATATGA 60.181 47.826 1.10 0.00 0.00 2.15
801 817 3.173965 ACTCCCTCCGTCCCATAATATG 58.826 50.000 0.00 0.00 0.00 1.78
802 818 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
803 819 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
804 820 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
805 821 4.140853 AGTTATACTCCCTCCGTCCCATAA 60.141 45.833 0.00 0.00 0.00 1.90
806 822 3.400322 AGTTATACTCCCTCCGTCCCATA 59.600 47.826 0.00 0.00 0.00 2.74
807 823 2.179424 AGTTATACTCCCTCCGTCCCAT 59.821 50.000 0.00 0.00 0.00 4.00
808 824 1.572415 AGTTATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
809 825 1.962100 CAGTTATACTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
810 826 2.941480 TCAGTTATACTCCCTCCGTCC 58.059 52.381 0.00 0.00 0.00 4.79
811 827 4.023021 GTCATCAGTTATACTCCCTCCGTC 60.023 50.000 0.00 0.00 0.00 4.79
812 828 3.890147 GTCATCAGTTATACTCCCTCCGT 59.110 47.826 0.00 0.00 0.00 4.69
813 829 4.145807 AGTCATCAGTTATACTCCCTCCG 58.854 47.826 0.00 0.00 0.00 4.63
814 830 7.067737 GCTATAGTCATCAGTTATACTCCCTCC 59.932 44.444 0.84 0.00 0.00 4.30
815 831 7.067737 GGCTATAGTCATCAGTTATACTCCCTC 59.932 44.444 0.00 0.00 0.00 4.30
816 832 6.893005 GGCTATAGTCATCAGTTATACTCCCT 59.107 42.308 0.00 0.00 0.00 4.20
817 833 6.097129 GGGCTATAGTCATCAGTTATACTCCC 59.903 46.154 6.69 0.00 0.00 4.30
818 834 6.663953 TGGGCTATAGTCATCAGTTATACTCC 59.336 42.308 6.69 0.00 0.00 3.85
819 835 7.176865 TGTGGGCTATAGTCATCAGTTATACTC 59.823 40.741 6.69 0.00 0.00 2.59
820 836 7.010771 TGTGGGCTATAGTCATCAGTTATACT 58.989 38.462 6.69 0.00 0.00 2.12
821 837 7.091443 GTGTGGGCTATAGTCATCAGTTATAC 58.909 42.308 6.69 0.00 0.00 1.47
826 842 2.362397 CGTGTGGGCTATAGTCATCAGT 59.638 50.000 6.69 0.00 0.00 3.41
827 843 2.288457 CCGTGTGGGCTATAGTCATCAG 60.288 54.545 6.69 0.00 0.00 2.90
860 876 8.262601 TGTAGATAAAAGGCTGAGATAATGGA 57.737 34.615 0.00 0.00 0.00 3.41
954 1000 2.099756 GGCATTGGGCTAGTGATTTGTC 59.900 50.000 0.00 0.00 44.01 3.18
1002 1048 4.025360 ACGGGGTTTTAAAAGTTTCTGGT 58.975 39.130 0.00 0.00 0.00 4.00
1063 1109 2.426305 GAAGGTGGTGGTGGGGAAGG 62.426 65.000 0.00 0.00 0.00 3.46
1069 1115 2.347490 CGAGGAAGGTGGTGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
1181 1227 1.831736 GAAACGGAGAAGGGAGATGGA 59.168 52.381 0.00 0.00 0.00 3.41
1299 1345 3.011517 CTCACCCCCTCCACCTGG 61.012 72.222 0.00 0.00 0.00 4.45
1316 1362 1.668151 GACACGTCCTCCTTGGTGC 60.668 63.158 0.00 0.00 37.07 5.01
1467 1513 4.717313 GTGGCGGGGAGGTTGGAC 62.717 72.222 0.00 0.00 0.00 4.02
1531 1578 1.448893 GCAAAGGGCACGACGGATA 60.449 57.895 0.00 0.00 43.97 2.59
1556 1603 3.066203 ACAAGAATCACCGGACAACAAAC 59.934 43.478 9.46 0.00 0.00 2.93
1558 1605 2.925724 ACAAGAATCACCGGACAACAA 58.074 42.857 9.46 0.00 0.00 2.83
1626 1673 6.875972 AGTATCAGGACACATTCTACCTTT 57.124 37.500 0.00 0.00 0.00 3.11
1660 1707 5.231357 ACACACATTATACGCACATAAGACG 59.769 40.000 0.00 0.00 0.00 4.18
1662 1709 7.603963 AAACACACATTATACGCACATAAGA 57.396 32.000 0.00 0.00 0.00 2.10
1669 1716 7.960195 CACTGAAATAAACACACATTATACGCA 59.040 33.333 0.00 0.00 0.00 5.24
1670 1717 8.172484 TCACTGAAATAAACACACATTATACGC 58.828 33.333 0.00 0.00 0.00 4.42
1686 1733 9.513906 TCTAAATGGACAACAATCACTGAAATA 57.486 29.630 0.00 0.00 0.00 1.40
1687 1734 8.408043 TCTAAATGGACAACAATCACTGAAAT 57.592 30.769 0.00 0.00 0.00 2.17
1688 1735 7.815840 TCTAAATGGACAACAATCACTGAAA 57.184 32.000 0.00 0.00 0.00 2.69
1689 1736 8.946085 GTATCTAAATGGACAACAATCACTGAA 58.054 33.333 0.00 0.00 0.00 3.02
1690 1737 7.552687 GGTATCTAAATGGACAACAATCACTGA 59.447 37.037 0.00 0.00 0.00 3.41
1691 1738 7.554118 AGGTATCTAAATGGACAACAATCACTG 59.446 37.037 0.00 0.00 0.00 3.66
1692 1739 7.633789 AGGTATCTAAATGGACAACAATCACT 58.366 34.615 0.00 0.00 0.00 3.41
1693 1740 7.865706 AGGTATCTAAATGGACAACAATCAC 57.134 36.000 0.00 0.00 0.00 3.06
1694 1741 7.709182 CGTAGGTATCTAAATGGACAACAATCA 59.291 37.037 0.00 0.00 0.00 2.57
1695 1742 7.924412 TCGTAGGTATCTAAATGGACAACAATC 59.076 37.037 0.00 0.00 0.00 2.67
1696 1743 7.709613 GTCGTAGGTATCTAAATGGACAACAAT 59.290 37.037 0.00 0.00 0.00 2.71
1771 1830 5.163642 ACACAGCAACCAAAACGTATAACAA 60.164 36.000 0.00 0.00 0.00 2.83
1879 1943 2.108250 GCATTTTATCTAGGGCCCCAGA 59.892 50.000 23.07 23.07 0.00 3.86
1880 1944 2.158475 TGCATTTTATCTAGGGCCCCAG 60.158 50.000 21.43 16.32 0.00 4.45
2021 2085 6.818644 CACCAGTCACTACATGCTAACTTTAT 59.181 38.462 0.00 0.00 0.00 1.40
2041 2105 3.181397 CACAGCAAACAAAACTCACCAG 58.819 45.455 0.00 0.00 0.00 4.00
2049 2113 4.753233 ACACAATAGCACAGCAAACAAAA 58.247 34.783 0.00 0.00 0.00 2.44
2062 2126 9.208022 TGATGCTAGAAATGTATACACAATAGC 57.792 33.333 22.26 22.26 38.42 2.97
2102 2166 8.040727 AGAGCTACCAAAATCAAACAAAAACTT 58.959 29.630 0.00 0.00 0.00 2.66
2103 2167 7.555965 AGAGCTACCAAAATCAAACAAAAACT 58.444 30.769 0.00 0.00 0.00 2.66
2152 2216 3.900703 GCGAAACAAAGACAAGTCGAATC 59.099 43.478 0.00 0.00 34.09 2.52
2157 2221 3.786048 CACAAGCGAAACAAAGACAAGTC 59.214 43.478 0.00 0.00 0.00 3.01
2173 2237 4.628333 AGTGCATGCATAATTTTCACAAGC 59.372 37.500 25.64 5.31 0.00 4.01
2182 2246 4.018490 TCTGGTTCAGTGCATGCATAATT 58.982 39.130 25.64 7.40 32.61 1.40
2183 2247 3.623703 TCTGGTTCAGTGCATGCATAAT 58.376 40.909 25.64 10.50 32.61 1.28
2185 2249 2.785540 TCTGGTTCAGTGCATGCATA 57.214 45.000 25.64 10.01 32.61 3.14
2189 2253 2.684881 GGGTTATCTGGTTCAGTGCATG 59.315 50.000 0.00 0.00 32.61 4.06
2193 2257 3.703001 ACAGGGTTATCTGGTTCAGTG 57.297 47.619 0.00 0.00 38.98 3.66
2238 2302 6.883756 TCACAATATTTACCAACTCTGATGCA 59.116 34.615 0.00 0.00 0.00 3.96
2294 2358 6.442513 AAACAGAAATAGTTCATGCCTAGC 57.557 37.500 5.62 0.00 36.09 3.42
2431 2496 7.564793 ACTATGAAACCACAGCACTTCATATA 58.435 34.615 4.36 0.00 39.07 0.86
2436 2501 4.091509 CGTACTATGAAACCACAGCACTTC 59.908 45.833 0.00 0.00 0.00 3.01
2443 2508 4.464951 ACATCCTCGTACTATGAAACCACA 59.535 41.667 0.00 0.00 0.00 4.17
2478 2543 4.673441 AGAATTGGTCGATGAGTAACTCG 58.327 43.478 0.00 0.00 36.25 4.18
2488 2553 2.026822 AGGCTGTGAAGAATTGGTCGAT 60.027 45.455 0.00 0.00 0.00 3.59
2566 2631 4.277174 ACGGTACAACAAGCAAATCAATCA 59.723 37.500 0.00 0.00 0.00 2.57
2588 2653 5.275494 ACCTAAACAACATGCGTACAAAAC 58.725 37.500 0.00 0.00 0.00 2.43
2591 2656 6.804770 AATACCTAAACAACATGCGTACAA 57.195 33.333 0.00 0.00 0.00 2.41
2593 2658 6.833839 TCAAATACCTAAACAACATGCGTAC 58.166 36.000 0.00 0.00 0.00 3.67
2597 2662 7.538575 ACATCTCAAATACCTAAACAACATGC 58.461 34.615 0.00 0.00 0.00 4.06
2598 2663 9.912634 AAACATCTCAAATACCTAAACAACATG 57.087 29.630 0.00 0.00 0.00 3.21
2649 2714 7.621796 TCTGGATTTCTAGACTTAAGGGAAAC 58.378 38.462 7.53 6.86 0.00 2.78
2650 2715 7.808279 TCTGGATTTCTAGACTTAAGGGAAA 57.192 36.000 7.53 11.32 0.00 3.13
2791 2857 8.645814 TTCAGGAAAAGAGACTACATAGTGTA 57.354 34.615 0.00 0.00 36.50 2.90
2792 2858 7.540474 TTCAGGAAAAGAGACTACATAGTGT 57.460 36.000 0.00 0.00 36.50 3.55
2842 2908 2.715046 TCTCACATTTCTGGGCATGTC 58.285 47.619 0.00 0.00 30.90 3.06
2871 2937 4.142924 GCAAAGAGAAAGAGAAGCACTAGC 60.143 45.833 0.00 0.00 42.56 3.42
2872 2938 4.993584 TGCAAAGAGAAAGAGAAGCACTAG 59.006 41.667 0.00 0.00 0.00 2.57
2873 2939 4.960938 TGCAAAGAGAAAGAGAAGCACTA 58.039 39.130 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.