Multiple sequence alignment - TraesCS2A01G239300

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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 TraesCS2A01G239300 chr2A 100.000 2339 0 0 1 2339 330396787 330399125 0.000000e+00 4320.0
1 TraesCS2A01G239300 chr2A 85.743 1473 179 22 864 2315 260774065 260772603 0.000000e+00 1528.0
2 TraesCS2A01G239300 chr2A 88.048 912 84 16 857 1764 388725677 388726567 0.000000e+00 1057.0
3 TraesCS2A01G239300 chr2A 86.606 769 86 16 1 762 234142209 234141451 0.000000e+00 833.0
4 TraesCS2A01G239300 chr2A 86.140 772 83 21 1 762 319918591 319917834 0.000000e+00 811.0
5 TraesCS2A01G239300 chr2A 85.974 770 89 18 1 762 234125771 234125013 0.000000e+00 806.0
6 TraesCS2A01G239300 chr2A 88.372 645 69 6 1673 2315 90304485 90303845 0.000000e+00 771.0
7 TraesCS2A01G239300 chr2A 88.395 405 26 10 730 1130 318953656 318953269 3.520000e-128 468.0
8 TraesCS2A01G239300 chr2A 85.145 276 36 5 857 1130 365656010 365656282 6.370000e-71 278.0
9 TraesCS2A01G239300 chr2A 83.962 212 25 9 730 936 723175501 723175708 6.600000e-46 195.0
10 TraesCS2A01G239300 chr2A 84.314 153 22 2 779 930 723167650 723167801 5.210000e-32 148.0
11 TraesCS2A01G239300 chr1A 85.831 1475 183 21 857 2315 297440353 297441817 0.000000e+00 1543.0
12 TraesCS2A01G239300 chr1A 86.234 770 88 17 1 762 219286473 219285714 0.000000e+00 819.0
13 TraesCS2A01G239300 chr1A 85.992 771 86 20 1 762 219269247 219268490 0.000000e+00 806.0
14 TraesCS2A01G239300 chr1A 87.393 698 78 9 1614 2307 312067854 312068545 0.000000e+00 793.0
15 TraesCS2A01G239300 chr1A 86.143 700 86 10 1614 2309 312059836 312060528 0.000000e+00 745.0
16 TraesCS2A01G239300 chr1A 100.000 29 0 0 2311 2339 523592685 523592713 1.000000e-03 54.7
17 TraesCS2A01G239300 chr7A 85.460 1458 188 21 872 2315 388332068 388333515 0.000000e+00 1496.0
18 TraesCS2A01G239300 chr7A 82.716 1458 193 39 866 2305 469678097 469676681 0.000000e+00 1242.0
19 TraesCS2A01G239300 chr7A 83.185 1350 193 27 982 2315 469695341 469694010 0.000000e+00 1205.0
20 TraesCS2A01G239300 chr7A 87.500 768 80 15 1 762 411635017 411635774 0.000000e+00 872.0
21 TraesCS2A01G239300 chr7A 88.000 675 69 10 1651 2317 445654254 445653584 0.000000e+00 787.0
22 TraesCS2A01G239300 chr7A 88.042 669 72 5 1653 2315 445712492 445711826 0.000000e+00 785.0
23 TraesCS2A01G239300 chr7A 87.594 266 31 2 866 1130 116711535 116711799 8.120000e-80 307.0
24 TraesCS2A01G239300 chr7A 88.123 261 28 2 872 1130 116727766 116728025 8.120000e-80 307.0
25 TraesCS2A01G239300 chr7A 90.385 156 14 1 1281 1435 32578523 32578368 1.100000e-48 204.0
26 TraesCS2A01G239300 chr7A 89.172 157 14 3 1281 1435 32540813 32540658 2.370000e-45 193.0
27 TraesCS2A01G239300 chr7A 100.000 29 0 0 2311 2339 80836587 80836615 1.000000e-03 54.7
28 TraesCS2A01G239300 chr7A 94.444 36 1 1 824 858 354279745 354279710 1.000000e-03 54.7
29 TraesCS2A01G239300 chr3A 88.010 784 74 19 1 773 384101780 384101006 0.000000e+00 909.0
30 TraesCS2A01G239300 chr3A 83.298 952 136 20 1381 2317 303330642 303329699 0.000000e+00 856.0
31 TraesCS2A01G239300 chr3A 90.835 611 53 3 1706 2315 194680846 194680238 0.000000e+00 815.0
32 TraesCS2A01G239300 chr3A 81.075 856 130 28 1474 2315 387259200 387258363 0.000000e+00 654.0
33 TraesCS2A01G239300 chr3A 100.000 29 0 0 2311 2339 354873161 354873133 1.000000e-03 54.7
34 TraesCS2A01G239300 chr5A 87.030 771 81 18 1 762 444509584 444510344 0.000000e+00 852.0
35 TraesCS2A01G239300 chr5A 86.381 771 86 18 1 762 444517517 444518277 0.000000e+00 824.0
36 TraesCS2A01G239300 chr5A 84.573 726 94 16 1598 2315 222622212 222621497 0.000000e+00 704.0
37 TraesCS2A01G239300 chr4A 83.353 853 116 21 1474 2316 481441220 481440384 0.000000e+00 765.0
38 TraesCS2A01G239300 chr4A 100.000 28 0 0 2312 2339 363988263 363988236 4.000000e-03 52.8
39 TraesCS2A01G239300 chr4B 91.358 243 20 1 1038 1279 429495923 429496165 4.820000e-87 331.0
40 TraesCS2A01G239300 chr4B 91.525 236 19 1 1045 1279 429503453 429503688 8.060000e-85 324.0
41 TraesCS2A01G239300 chr3B 90.947 243 20 2 1038 1279 239494407 239494166 2.240000e-85 326.0
42 TraesCS2A01G239300 chr6A 85.294 204 26 4 730 930 511724303 511724505 8.470000e-50 207.0
43 TraesCS2A01G239300 chr6A 97.143 35 1 0 824 858 341629776 341629742 2.510000e-05 60.2
44 TraesCS2A01G239300 chr3D 92.308 78 3 3 777 853 479346903 479346828 8.840000e-20 108.0
45 TraesCS2A01G239300 chr3D 100.000 29 0 0 2311 2339 555451390 555451418 1.000000e-03 54.7
46 TraesCS2A01G239300 chr7D 100.000 29 0 0 2311 2339 27053948 27053920 1.000000e-03 54.7
47 TraesCS2A01G239300 chr7B 96.970 33 0 1 2307 2339 64081577 64081546 1.000000e-03 54.7
48 TraesCS2A01G239300 chr6B 100.000 29 0 0 2311 2339 606829207 606829235 1.000000e-03 54.7
49 TraesCS2A01G239300 chr5B 100.000 28 0 0 2312 2339 655376063 655376036 4.000000e-03 52.8


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 TraesCS2A01G239300 chr2A 330396787 330399125 2338 False 4320 4320 100.000 1 2339 1 chr2A.!!$F1 2338
1 TraesCS2A01G239300 chr2A 260772603 260774065 1462 True 1528 1528 85.743 864 2315 1 chr2A.!!$R4 1451
2 TraesCS2A01G239300 chr2A 388725677 388726567 890 False 1057 1057 88.048 857 1764 1 chr2A.!!$F3 907
3 TraesCS2A01G239300 chr2A 234141451 234142209 758 True 833 833 86.606 1 762 1 chr2A.!!$R3 761
4 TraesCS2A01G239300 chr2A 319917834 319918591 757 True 811 811 86.140 1 762 1 chr2A.!!$R6 761
5 TraesCS2A01G239300 chr2A 234125013 234125771 758 True 806 806 85.974 1 762 1 chr2A.!!$R2 761
6 TraesCS2A01G239300 chr2A 90303845 90304485 640 True 771 771 88.372 1673 2315 1 chr2A.!!$R1 642
7 TraesCS2A01G239300 chr1A 297440353 297441817 1464 False 1543 1543 85.831 857 2315 1 chr1A.!!$F1 1458
8 TraesCS2A01G239300 chr1A 219285714 219286473 759 True 819 819 86.234 1 762 1 chr1A.!!$R2 761
9 TraesCS2A01G239300 chr1A 219268490 219269247 757 True 806 806 85.992 1 762 1 chr1A.!!$R1 761
10 TraesCS2A01G239300 chr1A 312067854 312068545 691 False 793 793 87.393 1614 2307 1 chr1A.!!$F3 693
11 TraesCS2A01G239300 chr1A 312059836 312060528 692 False 745 745 86.143 1614 2309 1 chr1A.!!$F2 695
12 TraesCS2A01G239300 chr7A 388332068 388333515 1447 False 1496 1496 85.460 872 2315 1 chr7A.!!$F4 1443
13 TraesCS2A01G239300 chr7A 469676681 469678097 1416 True 1242 1242 82.716 866 2305 1 chr7A.!!$R6 1439
14 TraesCS2A01G239300 chr7A 469694010 469695341 1331 True 1205 1205 83.185 982 2315 1 chr7A.!!$R7 1333
15 TraesCS2A01G239300 chr7A 411635017 411635774 757 False 872 872 87.500 1 762 1 chr7A.!!$F5 761
16 TraesCS2A01G239300 chr7A 445653584 445654254 670 True 787 787 88.000 1651 2317 1 chr7A.!!$R4 666
17 TraesCS2A01G239300 chr7A 445711826 445712492 666 True 785 785 88.042 1653 2315 1 chr7A.!!$R5 662
18 TraesCS2A01G239300 chr3A 384101006 384101780 774 True 909 909 88.010 1 773 1 chr3A.!!$R4 772
19 TraesCS2A01G239300 chr3A 303329699 303330642 943 True 856 856 83.298 1381 2317 1 chr3A.!!$R2 936
20 TraesCS2A01G239300 chr3A 194680238 194680846 608 True 815 815 90.835 1706 2315 1 chr3A.!!$R1 609
21 TraesCS2A01G239300 chr3A 387258363 387259200 837 True 654 654 81.075 1474 2315 1 chr3A.!!$R5 841
22 TraesCS2A01G239300 chr5A 444509584 444510344 760 False 852 852 87.030 1 762 1 chr5A.!!$F1 761
23 TraesCS2A01G239300 chr5A 444517517 444518277 760 False 824 824 86.381 1 762 1 chr5A.!!$F2 761
24 TraesCS2A01G239300 chr5A 222621497 222622212 715 True 704 704 84.573 1598 2315 1 chr5A.!!$R1 717
25 TraesCS2A01G239300 chr4A 481440384 481441220 836 True 765 765 83.353 1474 2316 1 chr4A.!!$R2 842

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
782 802 0.440371 GTTTCAGTGTAGCGAGCTGC 59.56 55.0 7.99 7.07 46.98 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1913 0.704076 ATGCCTACCCCTCTTTGCAA 59.296 50.0 0.0 0.0 31.81 4.08 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
171 179 4.022676 GTCAAGTTTAAATGAGGCCGGAAA 60.023 41.667 5.05 0.00 0.00 3.13
192 200 3.776340 ACAACAAACAACAATTCCGGAC 58.224 40.909 1.83 0.00 0.00 4.79
211 220 5.987953 CCGGACAATCCTCATATGCATATAG 59.012 44.000 18.70 14.94 33.30 1.31
220 230 8.435931 TCCTCATATGCATATAGTAGGTTTGT 57.564 34.615 26.07 3.09 31.35 2.83
239 250 3.746940 TGTTACTGTTCTGCCCTAAACC 58.253 45.455 0.00 0.00 0.00 3.27
256 267 8.528643 GCCCTAAACCATATTTTAGAGTTGTTT 58.471 33.333 8.04 0.00 40.24 2.83
273 284 8.466798 AGAGTTGTTTAACATGCAAAGTAAAGT 58.533 29.630 0.00 0.00 39.30 2.66
277 288 7.767261 TGTTTAACATGCAAAGTAAAGTCACT 58.233 30.769 0.00 0.00 0.00 3.41
279 290 9.166126 GTTTAACATGCAAAGTAAAGTCACTAC 57.834 33.333 0.00 0.00 0.00 2.73
286 297 8.145316 TGCAAAGTAAAGTCACTACGTTAAAT 57.855 30.769 0.00 0.00 32.47 1.40
346 358 6.070881 TGTTAGGTTTGGAGCTACGGTTATTA 60.071 38.462 0.00 0.00 35.71 0.98
602 619 3.543537 AAAAACACGCATGGGCCA 58.456 50.000 9.61 9.61 36.38 5.36
674 694 2.909965 TCCGCCCAAAACTGTGGC 60.910 61.111 0.00 0.00 41.85 5.01
745 765 2.624674 AAAGGTCAACGCAGCCTGGT 62.625 55.000 0.00 0.00 32.16 4.00
773 793 1.866601 TCGTCGTCTCGTTTCAGTGTA 59.133 47.619 0.00 0.00 0.00 2.90
774 794 2.096565 TCGTCGTCTCGTTTCAGTGTAG 60.097 50.000 0.00 0.00 0.00 2.74
775 795 1.977412 GTCGTCTCGTTTCAGTGTAGC 59.023 52.381 0.00 0.00 0.00 3.58
776 796 0.975544 CGTCTCGTTTCAGTGTAGCG 59.024 55.000 0.00 0.00 0.00 4.26
777 797 1.399343 CGTCTCGTTTCAGTGTAGCGA 60.399 52.381 8.30 8.30 0.00 4.93
778 798 2.243407 GTCTCGTTTCAGTGTAGCGAG 58.757 52.381 23.62 23.62 46.97 5.03
779 799 0.985549 CTCGTTTCAGTGTAGCGAGC 59.014 55.000 19.63 0.00 41.62 5.03
780 800 0.596577 TCGTTTCAGTGTAGCGAGCT 59.403 50.000 4.65 2.25 0.00 4.09
781 801 0.710567 CGTTTCAGTGTAGCGAGCTG 59.289 55.000 7.99 0.00 0.00 4.24
782 802 0.440371 GTTTCAGTGTAGCGAGCTGC 59.560 55.000 7.99 7.07 46.98 5.25
801 821 4.940593 GCGGCGCCTAGAGCAGAG 62.941 72.222 26.68 6.32 44.04 3.35
802 822 4.940593 CGGCGCCTAGAGCAGAGC 62.941 72.222 26.68 0.00 44.04 4.09
803 823 3.535962 GGCGCCTAGAGCAGAGCT 61.536 66.667 22.15 0.00 44.04 4.09
812 832 2.045829 AGCAGAGCTCCGACGAGA 60.046 61.111 10.93 0.00 38.52 4.04
813 833 2.112198 AGCAGAGCTCCGACGAGAG 61.112 63.158 10.93 2.53 38.52 3.20
814 834 3.106552 CAGAGCTCCGACGAGAGG 58.893 66.667 10.93 0.00 38.52 3.69
815 835 2.124487 AGAGCTCCGACGAGAGGG 60.124 66.667 10.93 0.00 38.52 4.30
816 836 3.894947 GAGCTCCGACGAGAGGGC 61.895 72.222 0.87 1.53 38.52 5.19
817 837 4.742649 AGCTCCGACGAGAGGGCA 62.743 66.667 13.06 0.00 38.52 5.36
818 838 3.760035 GCTCCGACGAGAGGGCAA 61.760 66.667 13.06 0.00 38.52 4.52
819 839 2.970639 CTCCGACGAGAGGGCAAA 59.029 61.111 0.00 0.00 38.52 3.68
820 840 1.153745 CTCCGACGAGAGGGCAAAG 60.154 63.158 0.00 0.00 38.52 2.77
821 841 1.878656 CTCCGACGAGAGGGCAAAGT 61.879 60.000 0.00 0.00 38.52 2.66
822 842 1.738099 CCGACGAGAGGGCAAAGTG 60.738 63.158 0.00 0.00 0.00 3.16
823 843 1.738099 CGACGAGAGGGCAAAGTGG 60.738 63.158 0.00 0.00 0.00 4.00
824 844 2.032681 ACGAGAGGGCAAAGTGGC 59.967 61.111 0.00 0.00 42.88 5.01
825 845 3.121030 CGAGAGGGCAAAGTGGCG 61.121 66.667 0.00 0.00 44.78 5.69
826 846 2.747855 GAGAGGGCAAAGTGGCGG 60.748 66.667 0.00 0.00 44.78 6.13
842 862 4.821589 GGCGAGGCGAGGGACTTG 62.822 72.222 0.00 0.00 41.55 3.16
843 863 4.821589 GCGAGGCGAGGGACTTGG 62.822 72.222 0.00 0.00 41.55 3.61
849 869 3.691342 CGAGGGACTTGGCGTGGA 61.691 66.667 0.00 0.00 41.55 4.02
850 870 2.266055 GAGGGACTTGGCGTGGAG 59.734 66.667 0.00 0.00 41.55 3.86
851 871 3.959991 GAGGGACTTGGCGTGGAGC 62.960 68.421 0.00 0.00 41.55 4.70
861 881 3.680786 CGTGGAGCGGTGACAGGA 61.681 66.667 0.00 0.00 36.85 3.86
862 882 2.048127 GTGGAGCGGTGACAGGAC 60.048 66.667 0.00 0.00 0.00 3.85
863 883 2.203640 TGGAGCGGTGACAGGACT 60.204 61.111 0.00 0.00 0.00 3.85
864 884 1.837051 TGGAGCGGTGACAGGACTT 60.837 57.895 0.00 0.00 0.00 3.01
891 911 4.035102 GGCGAACAGGGAAGGCCT 62.035 66.667 0.00 0.00 40.59 5.19
971 992 0.603569 AGGAAACGTGCATCTCGTCT 59.396 50.000 1.00 0.00 40.69 4.18
1025 1046 1.829533 CTGGTGCACTGGTGGCTTT 60.830 57.895 17.98 0.00 0.00 3.51
1029 1050 3.365265 GCACTGGTGGCTTTCGGG 61.365 66.667 2.84 0.00 0.00 5.14
1074 1095 2.355837 GACGCGCACAGAACTCCA 60.356 61.111 5.73 0.00 0.00 3.86
1095 1116 4.923942 AGGCGATGCAGATGCGGG 62.924 66.667 0.00 0.00 45.83 6.13
1100 1121 2.769621 ATGCAGATGCGGGGGAGA 60.770 61.111 0.00 0.00 45.83 3.71
1105 1126 2.836360 GATGCGGGGGAGACGGTA 60.836 66.667 0.00 0.00 0.00 4.02
1183 1211 1.407258 GAACAGAGAGGACGGGAGATG 59.593 57.143 0.00 0.00 0.00 2.90
1193 1221 2.235016 GACGGGAGATGCTAGAGTGAT 58.765 52.381 0.00 0.00 0.00 3.06
1227 1256 1.140134 CCAAGGGAGGAAGGGGACAA 61.140 60.000 0.00 0.00 0.00 3.18
1295 1324 1.541889 CGACATGGTCATGGATGAGGG 60.542 57.143 14.49 0.00 42.91 4.30
1343 1372 2.740714 GCAGGGACACGTGAATCGC 61.741 63.158 25.01 18.09 44.19 4.58
1399 1428 2.368878 GGGGATGAGGAGGCCCTT 60.369 66.667 0.00 0.00 44.53 3.95
1403 1432 1.148048 GATGAGGAGGCCCTTGAGC 59.852 63.158 0.00 0.00 44.53 4.26
1462 1491 4.856607 CGCGAAGGAGCTCCGGTC 62.857 72.222 26.95 24.60 42.08 4.79
1505 1534 0.976073 GAGGTGGACGAGGGGATCAA 60.976 60.000 0.00 0.00 0.00 2.57
1512 1541 1.383248 CGAGGGGATCAAGGGAGGT 60.383 63.158 0.00 0.00 0.00 3.85
1524 1554 2.829384 GGGAGGTGCTGGTTGGTGA 61.829 63.158 0.00 0.00 0.00 4.02
1533 1563 1.552337 GCTGGTTGGTGAGAGAGATCA 59.448 52.381 0.00 0.00 0.00 2.92
1576 1609 2.120909 CACACCGATTGGATGGGGC 61.121 63.158 5.81 0.00 39.21 5.80
1584 1617 0.703758 ATTGGATGGGGCTGGATCCT 60.704 55.000 14.23 0.00 39.23 3.24
1610 1648 4.802051 AGATGTGGCGGCGGCAAT 62.802 61.111 37.71 29.11 40.46 3.56
1668 1709 7.264947 GTTGCCCACTATTTATATTGCAAAGT 58.735 34.615 1.71 0.00 38.96 2.66
1687 1729 6.650120 CAAAGTGATTTAGGGTAGAGGCTAA 58.350 40.000 0.00 0.00 0.00 3.09
1718 1760 0.597637 GATCGCAATCGGATGGTCGT 60.598 55.000 8.38 0.00 36.13 4.34
1735 1779 6.474140 TGGTCGTGAATAAAATAGCTAGGA 57.526 37.500 0.00 0.00 0.00 2.94
1828 1880 1.374758 GTCAGGTCCGGAACAGCTG 60.375 63.158 24.28 17.92 40.16 4.24
1861 1913 1.545706 GGAGGAGGTCCGAAGCACTT 61.546 60.000 0.00 0.00 42.08 3.16
2171 2243 1.174712 GCATGCAAGTGTGTCTGGGT 61.175 55.000 14.21 0.00 0.00 4.51
2312 2389 3.436496 ACGACAGCGAATAACTAGAAGC 58.564 45.455 0.00 0.00 41.64 3.86
2313 2390 3.119602 ACGACAGCGAATAACTAGAAGCA 60.120 43.478 0.00 0.00 41.64 3.91
2314 2391 3.240861 CGACAGCGAATAACTAGAAGCAC 59.759 47.826 0.00 0.00 40.82 4.40
2316 2393 4.177026 ACAGCGAATAACTAGAAGCACTG 58.823 43.478 0.00 0.00 0.00 3.66
2318 2395 4.627467 CAGCGAATAACTAGAAGCACTGTT 59.373 41.667 0.00 0.00 0.00 3.16
2319 2396 4.865365 AGCGAATAACTAGAAGCACTGTTC 59.135 41.667 0.00 0.00 0.00 3.18
2320 2397 4.625742 GCGAATAACTAGAAGCACTGTTCA 59.374 41.667 0.00 0.00 0.00 3.18
2321 2398 5.120208 GCGAATAACTAGAAGCACTGTTCAA 59.880 40.000 0.00 0.00 0.00 2.69
2322 2399 6.670927 GCGAATAACTAGAAGCACTGTTCAAG 60.671 42.308 0.00 0.00 0.00 3.02
2323 2400 6.586463 CGAATAACTAGAAGCACTGTTCAAGA 59.414 38.462 0.00 0.00 0.00 3.02
2324 2401 7.116376 CGAATAACTAGAAGCACTGTTCAAGAA 59.884 37.037 0.00 0.00 0.00 2.52
2325 2402 8.854614 AATAACTAGAAGCACTGTTCAAGAAT 57.145 30.769 0.00 0.00 0.00 2.40
2326 2403 8.854614 ATAACTAGAAGCACTGTTCAAGAATT 57.145 30.769 0.00 0.00 0.00 2.17
2327 2404 6.793492 ACTAGAAGCACTGTTCAAGAATTC 57.207 37.500 0.00 0.00 0.00 2.17
2328 2405 6.291377 ACTAGAAGCACTGTTCAAGAATTCA 58.709 36.000 8.44 0.00 0.00 2.57
2329 2406 5.429957 AGAAGCACTGTTCAAGAATTCAC 57.570 39.130 8.44 0.00 0.00 3.18
2330 2407 4.276926 AGAAGCACTGTTCAAGAATTCACC 59.723 41.667 8.44 0.00 0.00 4.02
2331 2408 2.887152 AGCACTGTTCAAGAATTCACCC 59.113 45.455 8.44 0.00 0.00 4.61
2332 2409 2.350772 GCACTGTTCAAGAATTCACCCG 60.351 50.000 8.44 0.00 0.00 5.28
2333 2410 3.138304 CACTGTTCAAGAATTCACCCGA 58.862 45.455 8.44 0.00 0.00 5.14
2334 2411 3.753272 CACTGTTCAAGAATTCACCCGAT 59.247 43.478 8.44 0.00 0.00 4.18
2335 2412 4.216257 CACTGTTCAAGAATTCACCCGATT 59.784 41.667 8.44 0.00 0.00 3.34
2336 2413 5.411361 CACTGTTCAAGAATTCACCCGATTA 59.589 40.000 8.44 0.00 0.00 1.75
2337 2414 6.001460 ACTGTTCAAGAATTCACCCGATTAA 58.999 36.000 8.44 0.00 0.00 1.40
2338 2415 6.659242 ACTGTTCAAGAATTCACCCGATTAAT 59.341 34.615 8.44 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 179 3.193691 TGTCCGGAATTGTTGTTTGTTGT 59.806 39.130 5.23 0.00 0.00 3.32
192 200 9.896645 AAACCTACTATATGCATATGAGGATTG 57.103 33.333 31.22 17.78 0.00 2.67
211 220 3.501062 GGGCAGAACAGTAACAAACCTAC 59.499 47.826 0.00 0.00 0.00 3.18
220 230 4.650972 ATGGTTTAGGGCAGAACAGTAA 57.349 40.909 0.00 0.00 0.00 2.24
256 267 6.702723 ACGTAGTGACTTTACTTTGCATGTTA 59.297 34.615 0.00 0.00 42.51 2.41
269 280 7.916914 ATGCCTAATTTAACGTAGTGACTTT 57.083 32.000 0.00 0.00 45.00 2.66
271 282 7.916914 AAATGCCTAATTTAACGTAGTGACT 57.083 32.000 0.00 0.00 36.46 3.41
273 284 9.005777 AGAAAAATGCCTAATTTAACGTAGTGA 57.994 29.630 0.00 0.00 37.32 3.41
277 288 8.676401 GGGTAGAAAAATGCCTAATTTAACGTA 58.324 33.333 0.00 0.00 37.51 3.57
279 290 6.976349 GGGGTAGAAAAATGCCTAATTTAACG 59.024 38.462 0.00 0.00 37.51 3.18
286 297 6.954684 TGTAAATGGGGTAGAAAAATGCCTAA 59.045 34.615 0.00 0.00 0.00 2.69
326 338 5.181009 ACTTAATAACCGTAGCTCCAAACC 58.819 41.667 0.00 0.00 0.00 3.27
398 411 8.547069 CATCCACGTTTGAAATGTTTAAAATGT 58.453 29.630 0.00 7.16 39.96 2.71
401 415 8.703604 TTCATCCACGTTTGAAATGTTTAAAA 57.296 26.923 0.00 0.00 0.00 1.52
413 427 1.336440 TGCCACTTTCATCCACGTTTG 59.664 47.619 0.00 0.00 0.00 2.93
665 685 1.674057 CTCCTCCTCGCCACAGTTT 59.326 57.895 0.00 0.00 0.00 2.66
715 735 1.128692 GTTGACCTTTCAATCGAGCCG 59.871 52.381 0.00 0.00 43.72 5.52
724 744 1.148273 AGGCTGCGTTGACCTTTCA 59.852 52.632 0.00 0.00 0.00 2.69
749 769 2.765922 GAAACGAGACGACGAGCGC 61.766 63.158 0.00 0.00 46.04 5.92
758 778 2.327081 TCGCTACACTGAAACGAGAC 57.673 50.000 0.00 0.00 0.00 3.36
784 804 4.940593 CTCTGCTCTAGGCGCCGC 62.941 72.222 23.20 19.20 45.43 6.53
785 805 4.940593 GCTCTGCTCTAGGCGCCG 62.941 72.222 23.20 8.11 45.43 6.46
786 806 3.535962 AGCTCTGCTCTAGGCGCC 61.536 66.667 21.89 21.89 45.43 6.53
795 815 2.045829 TCTCGTCGGAGCTCTGCT 60.046 61.111 18.28 0.00 43.88 4.24
796 816 2.407210 CTCTCGTCGGAGCTCTGC 59.593 66.667 18.28 11.77 40.26 4.26
797 817 2.477176 CCCTCTCGTCGGAGCTCTG 61.477 68.421 16.98 16.98 40.26 3.35
798 818 2.124487 CCCTCTCGTCGGAGCTCT 60.124 66.667 14.64 0.00 40.26 4.09
799 819 3.894947 GCCCTCTCGTCGGAGCTC 61.895 72.222 4.71 4.71 40.26 4.09
800 820 4.742649 TGCCCTCTCGTCGGAGCT 62.743 66.667 0.00 0.00 40.26 4.09
801 821 3.296709 TTTGCCCTCTCGTCGGAGC 62.297 63.158 5.50 0.00 40.26 4.70
802 822 1.153745 CTTTGCCCTCTCGTCGGAG 60.154 63.158 0.00 0.00 41.89 4.63
803 823 1.906824 ACTTTGCCCTCTCGTCGGA 60.907 57.895 0.00 0.00 0.00 4.55
804 824 1.738099 CACTTTGCCCTCTCGTCGG 60.738 63.158 0.00 0.00 0.00 4.79
805 825 1.738099 CCACTTTGCCCTCTCGTCG 60.738 63.158 0.00 0.00 0.00 5.12
806 826 2.035442 GCCACTTTGCCCTCTCGTC 61.035 63.158 0.00 0.00 0.00 4.20
807 827 2.032681 GCCACTTTGCCCTCTCGT 59.967 61.111 0.00 0.00 0.00 4.18
808 828 3.121030 CGCCACTTTGCCCTCTCG 61.121 66.667 0.00 0.00 0.00 4.04
809 829 2.747855 CCGCCACTTTGCCCTCTC 60.748 66.667 0.00 0.00 0.00 3.20
825 845 4.821589 CAAGTCCCTCGCCTCGCC 62.822 72.222 0.00 0.00 0.00 5.54
826 846 4.821589 CCAAGTCCCTCGCCTCGC 62.822 72.222 0.00 0.00 0.00 5.03
827 847 4.821589 GCCAAGTCCCTCGCCTCG 62.822 72.222 0.00 0.00 0.00 4.63
828 848 4.821589 CGCCAAGTCCCTCGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
832 852 3.649277 CTCCACGCCAAGTCCCTCG 62.649 68.421 0.00 0.00 0.00 4.63
833 853 2.266055 CTCCACGCCAAGTCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
834 854 4.021925 GCTCCACGCCAAGTCCCT 62.022 66.667 0.00 0.00 0.00 4.20
837 857 4.681978 ACCGCTCCACGCCAAGTC 62.682 66.667 0.00 0.00 41.76 3.01
838 858 4.988598 CACCGCTCCACGCCAAGT 62.989 66.667 0.00 0.00 41.76 3.16
839 859 4.680237 TCACCGCTCCACGCCAAG 62.680 66.667 0.00 0.00 41.76 3.61
840 860 4.980805 GTCACCGCTCCACGCCAA 62.981 66.667 0.00 0.00 41.76 4.52
844 864 3.680786 TCCTGTCACCGCTCCACG 61.681 66.667 0.00 0.00 43.15 4.94
845 865 2.048127 GTCCTGTCACCGCTCCAC 60.048 66.667 0.00 0.00 0.00 4.02
846 866 1.837051 AAGTCCTGTCACCGCTCCA 60.837 57.895 0.00 0.00 0.00 3.86
847 867 1.374758 CAAGTCCTGTCACCGCTCC 60.375 63.158 0.00 0.00 0.00 4.70
848 868 2.029844 GCAAGTCCTGTCACCGCTC 61.030 63.158 0.00 0.00 0.00 5.03
849 869 2.031163 GCAAGTCCTGTCACCGCT 59.969 61.111 0.00 0.00 0.00 5.52
850 870 3.414700 CGCAAGTCCTGTCACCGC 61.415 66.667 0.00 0.00 0.00 5.68
851 871 2.738521 CCGCAAGTCCTGTCACCG 60.739 66.667 0.00 0.00 0.00 4.94
852 872 3.050275 GCCGCAAGTCCTGTCACC 61.050 66.667 0.00 0.00 0.00 4.02
853 873 3.414700 CGCCGCAAGTCCTGTCAC 61.415 66.667 0.00 0.00 0.00 3.67
854 874 4.680237 CCGCCGCAAGTCCTGTCA 62.680 66.667 0.00 0.00 0.00 3.58
891 911 3.062466 CGGAGACTGGTCCTCGCA 61.062 66.667 0.00 0.00 34.00 5.10
971 992 1.218047 CTCTGCATCGAACGGGGAA 59.782 57.895 0.00 0.00 0.00 3.97
1063 1084 1.739562 GCCTCGCTGGAGTTCTGTG 60.740 63.158 0.00 0.00 38.70 3.66
1069 1090 4.521062 GCATCGCCTCGCTGGAGT 62.521 66.667 0.00 0.00 38.70 3.85
1074 1095 2.279985 CATCTGCATCGCCTCGCT 60.280 61.111 0.00 0.00 0.00 4.93
1183 1211 6.952773 TCCTCTTCTCTTTATCACTCTAGC 57.047 41.667 0.00 0.00 0.00 3.42
1193 1221 4.499472 TCCCTTGGTTCCTCTTCTCTTTA 58.501 43.478 0.00 0.00 0.00 1.85
1227 1256 1.076339 CTCGCCTCCCTTCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
1271 1300 1.971505 ATCCATGACCATGTCGCCGT 61.972 55.000 8.93 0.00 37.11 5.68
1343 1372 0.671781 CTCCAGTCGCCTTCAACCAG 60.672 60.000 0.00 0.00 0.00 4.00
1373 1402 2.825836 CTCATCCCCAACCAGCGC 60.826 66.667 0.00 0.00 0.00 5.92
1505 1534 2.450502 ACCAACCAGCACCTCCCT 60.451 61.111 0.00 0.00 0.00 4.20
1512 1541 1.552337 GATCTCTCTCACCAACCAGCA 59.448 52.381 0.00 0.00 0.00 4.41
1524 1554 6.462768 CGATCCAAAATCCTCTTGATCTCTCT 60.463 42.308 0.00 0.00 31.61 3.10
1533 1563 2.092375 GTCCCCGATCCAAAATCCTCTT 60.092 50.000 0.00 0.00 0.00 2.85
1563 1596 0.607489 GATCCAGCCCCATCCAATCG 60.607 60.000 0.00 0.00 0.00 3.34
1576 1609 0.031716 TCTCCCACCTCAGGATCCAG 60.032 60.000 15.82 6.08 31.48 3.86
1584 1617 2.659063 CGCCACATCTCCCACCTCA 61.659 63.158 0.00 0.00 0.00 3.86
1608 1646 3.624777 GACATTGTCCCATCCACTCATT 58.375 45.455 5.44 0.00 0.00 2.57
1610 1648 1.281867 GGACATTGTCCCATCCACTCA 59.718 52.381 23.00 0.00 46.19 3.41
1668 1709 4.098960 CGTGTTAGCCTCTACCCTAAATCA 59.901 45.833 0.00 0.00 0.00 2.57
1718 1760 9.920946 AATTGGACTTCCTAGCTATTTTATTCA 57.079 29.630 0.00 0.00 36.82 2.57
1735 1779 8.575649 ACATCTCCGTTTTATTAATTGGACTT 57.424 30.769 0.00 0.00 0.00 3.01
1767 1811 2.158475 GCCTGGATCATCCCCAAACATA 60.158 50.000 0.00 0.00 35.03 2.29
1861 1913 0.704076 ATGCCTACCCCTCTTTGCAA 59.296 50.000 0.00 0.00 31.81 4.08
1967 2036 1.774639 TAGTCGGTCAAAACGTCAGC 58.225 50.000 0.00 0.00 0.00 4.26
2059 2131 4.025979 GCGTGTGGTCTTATTATAGTGCAC 60.026 45.833 9.40 9.40 0.00 4.57
2061 2133 3.493503 GGCGTGTGGTCTTATTATAGTGC 59.506 47.826 0.00 0.00 0.00 4.40
2154 2226 1.133823 TGAACCCAGACACACTTGCAT 60.134 47.619 0.00 0.00 0.00 3.96
2171 2243 4.131649 TCTTTCTGTTGTCCGTTCTGAA 57.868 40.909 0.00 0.00 0.00 3.02
2312 2389 3.138304 TCGGGTGAATTCTTGAACAGTG 58.862 45.455 7.05 0.00 0.00 3.66
2313 2390 3.485463 TCGGGTGAATTCTTGAACAGT 57.515 42.857 7.05 0.00 0.00 3.55
2314 2391 6.494893 TTAATCGGGTGAATTCTTGAACAG 57.505 37.500 7.05 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.