Multiple sequence alignment - TraesCS4A01G318400

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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 TraesCS4A01G318400 chr4A 100.000 3506 0 0 1 3506 607308139 607311644 0.000000e+00 6475.0
1 TraesCS4A01G318400 chr4A 79.630 108 15 5 713 816 101954245 101954349 1.750000e-08 71.3
2 TraesCS4A01G318400 chrUn 93.919 1776 81 9 750 2514 67470954 67469195 0.000000e+00 2656.0
3 TraesCS4A01G318400 chrUn 93.628 769 45 2 1 765 67471737 67470969 0.000000e+00 1146.0
4 TraesCS4A01G318400 chrUn 87.008 839 84 12 1 818 2577104 2576270 0.000000e+00 922.0
5 TraesCS4A01G318400 chr5D 92.768 1756 99 11 899 2650 565786925 565785194 0.000000e+00 2514.0
6 TraesCS4A01G318400 chr5D 89.394 66 7 0 996 1061 565790927 565790862 2.240000e-12 84.2
7 TraesCS4A01G318400 chr2A 89.129 1481 131 20 996 2472 211459905 211461359 0.000000e+00 1816.0
8 TraesCS4A01G318400 chr2A 80.796 1458 207 45 1042 2466 210751182 210749765 0.000000e+00 1074.0
9 TraesCS4A01G318400 chr2A 81.724 963 143 20 1052 2002 211482523 211483464 0.000000e+00 773.0
10 TraesCS4A01G318400 chr2A 84.507 497 74 3 1507 2002 211695183 211694689 4.070000e-134 488.0
11 TraesCS4A01G318400 chr2A 81.022 137 26 0 1056 1192 211695590 211695454 3.700000e-20 110.0
12 TraesCS4A01G318400 chr2D 88.783 1471 124 20 1002 2472 195995110 195996539 0.000000e+00 1764.0
13 TraesCS4A01G318400 chr2D 97.683 777 12 1 2729 3505 567472143 567472913 0.000000e+00 1330.0
14 TraesCS4A01G318400 chr2D 97.429 778 20 0 2729 3506 166572067 166571290 0.000000e+00 1327.0
15 TraesCS4A01G318400 chr2D 80.959 1460 201 48 1042 2466 195423267 195421850 0.000000e+00 1085.0
16 TraesCS4A01G318400 chr2D 82.034 590 92 10 1414 2002 196131100 196130524 1.130000e-134 490.0
17 TraesCS4A01G318400 chr2D 85.044 341 51 0 2113 2453 196002534 196002874 7.200000e-92 348.0
18 TraesCS4A01G318400 chr2D 81.752 137 25 0 1056 1192 196131425 196131289 7.950000e-22 115.0
19 TraesCS4A01G318400 chr5B 98.201 778 14 0 2729 3506 669549913 669550690 0.000000e+00 1360.0
20 TraesCS4A01G318400 chr5B 93.628 769 45 2 1 765 707361085 707360317 0.000000e+00 1146.0
21 TraesCS4A01G318400 chr5B 93.663 647 23 6 750 1391 707360302 707359669 0.000000e+00 952.0
22 TraesCS4A01G318400 chr5B 87.605 831 79 11 8 819 403154096 403154921 0.000000e+00 942.0
23 TraesCS4A01G318400 chr5B 87.410 834 83 10 3 818 614364090 614364919 0.000000e+00 939.0
24 TraesCS4A01G318400 chr5B 90.756 595 44 7 2061 2650 707391216 707391804 0.000000e+00 784.0
25 TraesCS4A01G318400 chr5B 94.118 459 24 2 2061 2519 707359655 707359200 0.000000e+00 695.0
26 TraesCS4A01G318400 chr4B 98.072 778 15 0 2729 3506 119331286 119330509 0.000000e+00 1354.0
27 TraesCS4A01G318400 chr4B 86.858 837 85 11 1 817 599082927 599082096 0.000000e+00 913.0
28 TraesCS4A01G318400 chr4B 85.290 775 89 11 66 819 659332662 659333432 0.000000e+00 776.0
29 TraesCS4A01G318400 chr4B 77.778 783 141 24 2746 3506 631547061 631547832 5.340000e-123 451.0
30 TraesCS4A01G318400 chr6A 97.815 778 17 0 2729 3506 501169186 501169963 0.000000e+00 1343.0
31 TraesCS4A01G318400 chr2B 80.585 1437 197 47 1042 2449 251771557 251770174 0.000000e+00 1033.0
32 TraesCS4A01G318400 chr2B 83.114 835 119 9 6 820 671256022 671256854 0.000000e+00 741.0
33 TraesCS4A01G318400 chr6B 89.065 759 78 3 1 755 719751656 719752413 0.000000e+00 937.0
34 TraesCS4A01G318400 chr6B 87.305 835 85 9 1 817 679677671 679676840 0.000000e+00 935.0
35 TraesCS4A01G318400 chr6B 86.463 820 87 13 18 818 693128275 693127461 0.000000e+00 878.0
36 TraesCS4A01G318400 chr4D 86.114 821 106 5 1 817 443712598 443713414 0.000000e+00 878.0
37 TraesCS4A01G318400 chr3B 84.505 839 106 12 1 820 679196546 679195713 0.000000e+00 808.0
38 TraesCS4A01G318400 chr3B 89.189 74 8 0 2744 2817 809167281 809167208 3.730000e-15 93.5
39 TraesCS4A01G318400 chr7A 78.002 891 151 29 1116 1991 680629848 680628988 5.190000e-143 518.0
40 TraesCS4A01G318400 chr1B 77.650 783 146 19 2744 3506 476346795 476346022 1.920000e-122 449.0
41 TraesCS4A01G318400 chr1B 80.402 199 37 2 2124 2322 675790243 675790047 2.180000e-32 150.0
42 TraesCS4A01G318400 chr7D 82.192 365 44 10 475 820 613458494 613458132 9.520000e-76 294.0
43 TraesCS4A01G318400 chr1A 76.106 339 73 6 2127 2460 582694177 582693842 1.670000e-38 171.0
44 TraesCS4A01G318400 chr5A 98.701 77 1 0 2650 2726 687221255 687221179 1.700000e-28 137.0
45 TraesCS4A01G318400 chr1D 79.375 160 31 2 2744 2902 354723181 354723023 1.030000e-20 111.0


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 TraesCS4A01G318400 chr4A 607308139 607311644 3505 False 6475.0 6475 100.0000 1 3506 1 chr4A.!!$F2 3505
1 TraesCS4A01G318400 chrUn 67469195 67471737 2542 True 1901.0 2656 93.7735 1 2514 2 chrUn.!!$R2 2513
2 TraesCS4A01G318400 chrUn 2576270 2577104 834 True 922.0 922 87.0080 1 818 1 chrUn.!!$R1 817
3 TraesCS4A01G318400 chr5D 565785194 565790927 5733 True 1299.1 2514 91.0810 899 2650 2 chr5D.!!$R1 1751
4 TraesCS4A01G318400 chr2A 211459905 211461359 1454 False 1816.0 1816 89.1290 996 2472 1 chr2A.!!$F1 1476
5 TraesCS4A01G318400 chr2A 210749765 210751182 1417 True 1074.0 1074 80.7960 1042 2466 1 chr2A.!!$R1 1424
6 TraesCS4A01G318400 chr2A 211482523 211483464 941 False 773.0 773 81.7240 1052 2002 1 chr2A.!!$F2 950
7 TraesCS4A01G318400 chr2A 211694689 211695590 901 True 299.0 488 82.7645 1056 2002 2 chr2A.!!$R2 946
8 TraesCS4A01G318400 chr2D 195995110 195996539 1429 False 1764.0 1764 88.7830 1002 2472 1 chr2D.!!$F1 1470
9 TraesCS4A01G318400 chr2D 567472143 567472913 770 False 1330.0 1330 97.6830 2729 3505 1 chr2D.!!$F3 776
10 TraesCS4A01G318400 chr2D 166571290 166572067 777 True 1327.0 1327 97.4290 2729 3506 1 chr2D.!!$R1 777
11 TraesCS4A01G318400 chr2D 195421850 195423267 1417 True 1085.0 1085 80.9590 1042 2466 1 chr2D.!!$R2 1424
12 TraesCS4A01G318400 chr2D 196130524 196131425 901 True 302.5 490 81.8930 1056 2002 2 chr2D.!!$R3 946
13 TraesCS4A01G318400 chr5B 669549913 669550690 777 False 1360.0 1360 98.2010 2729 3506 1 chr5B.!!$F3 777
14 TraesCS4A01G318400 chr5B 403154096 403154921 825 False 942.0 942 87.6050 8 819 1 chr5B.!!$F1 811
15 TraesCS4A01G318400 chr5B 614364090 614364919 829 False 939.0 939 87.4100 3 818 1 chr5B.!!$F2 815
16 TraesCS4A01G318400 chr5B 707359200 707361085 1885 True 931.0 1146 93.8030 1 2519 3 chr5B.!!$R1 2518
17 TraesCS4A01G318400 chr5B 707391216 707391804 588 False 784.0 784 90.7560 2061 2650 1 chr5B.!!$F4 589
18 TraesCS4A01G318400 chr4B 119330509 119331286 777 True 1354.0 1354 98.0720 2729 3506 1 chr4B.!!$R1 777
19 TraesCS4A01G318400 chr4B 599082096 599082927 831 True 913.0 913 86.8580 1 817 1 chr4B.!!$R2 816
20 TraesCS4A01G318400 chr4B 659332662 659333432 770 False 776.0 776 85.2900 66 819 1 chr4B.!!$F2 753
21 TraesCS4A01G318400 chr4B 631547061 631547832 771 False 451.0 451 77.7780 2746 3506 1 chr4B.!!$F1 760
22 TraesCS4A01G318400 chr6A 501169186 501169963 777 False 1343.0 1343 97.8150 2729 3506 1 chr6A.!!$F1 777
23 TraesCS4A01G318400 chr2B 251770174 251771557 1383 True 1033.0 1033 80.5850 1042 2449 1 chr2B.!!$R1 1407
24 TraesCS4A01G318400 chr2B 671256022 671256854 832 False 741.0 741 83.1140 6 820 1 chr2B.!!$F1 814
25 TraesCS4A01G318400 chr6B 719751656 719752413 757 False 937.0 937 89.0650 1 755 1 chr6B.!!$F1 754
26 TraesCS4A01G318400 chr6B 679676840 679677671 831 True 935.0 935 87.3050 1 817 1 chr6B.!!$R1 816
27 TraesCS4A01G318400 chr6B 693127461 693128275 814 True 878.0 878 86.4630 18 818 1 chr6B.!!$R2 800
28 TraesCS4A01G318400 chr4D 443712598 443713414 816 False 878.0 878 86.1140 1 817 1 chr4D.!!$F1 816
29 TraesCS4A01G318400 chr3B 679195713 679196546 833 True 808.0 808 84.5050 1 820 1 chr3B.!!$R1 819
30 TraesCS4A01G318400 chr7A 680628988 680629848 860 True 518.0 518 78.0020 1116 1991 1 chr7A.!!$R1 875
31 TraesCS4A01G318400 chr1B 476346022 476346795 773 True 449.0 449 77.6500 2744 3506 1 chr1B.!!$R1 762

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
579 586 1.202675 TCGTTCAACGGTAAGGGCTTT 60.203 47.619 10.69 0.00 42.81 3.51 F
1242 4351 0.319555 ATACGATTGTCATCCGGCGG 60.320 55.000 22.51 22.51 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 4831 0.108207 GGTGGATGATGCCTCTCCAG 59.892 60.0 9.35 0.0 39.66 3.86 R
2660 5874 0.174845 TAGTGCCCGTCGATTTGAGG 59.825 55.0 0.00 0.0 0.00 3.86 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
46 49 2.827921 GGAAATGCCAATCTTCCAGTGT 59.172 45.455 0.00 0.00 38.80 3.55
101 104 2.203098 CGTTGGTTGTGACGGGGT 60.203 61.111 0.00 0.00 35.74 4.95
122 125 2.342279 CCGGATCCACACGTGTGT 59.658 61.111 38.40 26.17 46.17 3.72
154 159 4.327680 ACTCCCTTGCAGTCTATGTTTTC 58.672 43.478 0.00 0.00 0.00 2.29
160 166 3.754965 TGCAGTCTATGTTTTCAGGCTT 58.245 40.909 0.00 0.00 0.00 4.35
378 385 2.738521 GCGTCGGCAGAAGCTTGA 60.739 61.111 16.61 0.00 46.09 3.02
543 550 2.207229 CGATGGCCTGTCCGGGATA 61.207 63.158 3.32 0.00 37.80 2.59
579 586 1.202675 TCGTTCAACGGTAAGGGCTTT 60.203 47.619 10.69 0.00 42.81 3.51
659 669 1.223763 GTTCGGGGGAGGTGATTCC 59.776 63.158 0.00 0.00 36.46 3.01
850 891 5.571784 ATTCGAGTAGAACCGTTGTGATA 57.428 39.130 0.00 0.00 42.39 2.15
879 920 6.954684 AGAGTCCGGGTAGAATATATCAATGT 59.045 38.462 0.00 0.00 0.00 2.71
914 4019 8.489990 TGATTCTTCTTCTTCTTCTGCAATAG 57.510 34.615 0.00 0.00 0.00 1.73
951 4060 4.111016 TGAGGACGTACGCTGGCG 62.111 66.667 16.72 13.56 46.03 5.69
1153 4262 3.700831 GAGCTCCTCCCCGACGAGA 62.701 68.421 0.87 0.00 30.97 4.04
1227 4336 2.580470 CGAGAAGCAGCGGCATACG 61.580 63.158 12.44 7.41 44.61 3.06
1242 4351 0.319555 ATACGATTGTCATCCGGCGG 60.320 55.000 22.51 22.51 0.00 6.13
1317 4450 4.436998 GCGCTCACGTACCTGGCT 62.437 66.667 0.00 0.00 42.83 4.75
1589 4770 1.838112 GTGCCCTTCATCATGTCCAA 58.162 50.000 0.00 0.00 0.00 3.53
1664 4848 0.758310 TCGAGCTGGAGAGGCATCAT 60.758 55.000 0.00 0.00 0.00 2.45
1704 4888 2.434185 GACACGCTCGCCATGGAA 60.434 61.111 18.40 0.73 0.00 3.53
1803 4987 1.951631 GTGGAAGCGCGGCTATCTC 60.952 63.158 8.83 0.26 38.25 2.75
1888 5072 2.872732 TCAACCTCTACGACCTTGACT 58.127 47.619 0.00 0.00 0.00 3.41
1899 5083 1.192803 ACCTTGACTTCTCCGGGGTC 61.193 60.000 0.00 6.05 0.00 4.46
2298 5502 2.669569 GCCTTCAAGACGCTGGCA 60.670 61.111 0.00 0.00 42.79 4.92
2313 5517 1.373812 GGCACGGAACTACCACCTT 59.626 57.895 0.00 0.00 38.90 3.50
2344 5548 1.319541 CGCTCTCTTCCCGGAGATTA 58.680 55.000 0.73 0.00 40.92 1.75
2379 5589 4.382320 GTGGAGGTTACGCCGGCA 62.382 66.667 28.98 4.32 43.70 5.69
2453 5663 4.202461 TGTGCTTATGGAGTTCCTCAAAGT 60.202 41.667 0.00 0.00 36.82 2.66
2481 5691 2.529151 AGCAAAACAAACGACAAGCAG 58.471 42.857 0.00 0.00 0.00 4.24
2482 5692 1.006079 GCAAAACAAACGACAAGCAGC 60.006 47.619 0.00 0.00 0.00 5.25
2483 5693 2.257894 CAAAACAAACGACAAGCAGCA 58.742 42.857 0.00 0.00 0.00 4.41
2526 5740 1.835494 TAGCAGAGACGGCTAGTTGT 58.165 50.000 0.00 0.00 42.62 3.32
2555 5769 3.004171 TGTTGCAACCGGTCATACATAC 58.996 45.455 26.14 0.00 0.00 2.39
2556 5770 3.267483 GTTGCAACCGGTCATACATACT 58.733 45.455 19.15 0.00 0.00 2.12
2557 5771 2.899976 TGCAACCGGTCATACATACTG 58.100 47.619 8.04 0.00 0.00 2.74
2570 5784 9.931210 GGTCATACATACTGTAACAATTTTAGC 57.069 33.333 0.00 0.00 36.31 3.09
2582 5796 8.185505 TGTAACAATTTTAGCGGTTCAATATCC 58.814 33.333 0.00 0.00 0.00 2.59
2591 5805 2.800544 CGGTTCAATATCCATCGTGTCC 59.199 50.000 0.00 0.00 0.00 4.02
2593 5807 2.800544 GTTCAATATCCATCGTGTCCGG 59.199 50.000 0.00 0.00 33.95 5.14
2594 5808 1.148310 CAATATCCATCGTGTCCGGC 58.852 55.000 0.00 0.00 33.95 6.13
2595 5809 0.756294 AATATCCATCGTGTCCGGCA 59.244 50.000 0.00 0.00 33.95 5.69
2596 5810 0.976641 ATATCCATCGTGTCCGGCAT 59.023 50.000 0.00 0.00 33.95 4.40
2650 5864 8.548877 TGAGTTTTGATTTTAGGCTAGATAGGT 58.451 33.333 0.00 0.00 0.00 3.08
2651 5865 8.738645 AGTTTTGATTTTAGGCTAGATAGGTG 57.261 34.615 0.00 0.00 0.00 4.00
2652 5866 7.775561 AGTTTTGATTTTAGGCTAGATAGGTGG 59.224 37.037 0.00 0.00 0.00 4.61
2653 5867 5.825593 TGATTTTAGGCTAGATAGGTGGG 57.174 43.478 0.00 0.00 0.00 4.61
2654 5868 5.224441 TGATTTTAGGCTAGATAGGTGGGT 58.776 41.667 0.00 0.00 0.00 4.51
2655 5869 5.307196 TGATTTTAGGCTAGATAGGTGGGTC 59.693 44.000 0.00 0.00 0.00 4.46
2656 5870 3.985553 TTAGGCTAGATAGGTGGGTCA 57.014 47.619 0.00 0.00 0.00 4.02
2657 5871 4.487282 TTAGGCTAGATAGGTGGGTCAT 57.513 45.455 0.00 0.00 0.00 3.06
2658 5872 2.896039 AGGCTAGATAGGTGGGTCATC 58.104 52.381 0.00 0.00 0.00 2.92
2659 5873 1.546476 GGCTAGATAGGTGGGTCATCG 59.454 57.143 0.00 0.00 0.00 3.84
2660 5874 1.067495 GCTAGATAGGTGGGTCATCGC 60.067 57.143 0.00 0.00 0.00 4.58
2661 5875 1.546476 CTAGATAGGTGGGTCATCGCC 59.454 57.143 0.00 0.00 37.57 5.54
2663 5877 0.318762 GATAGGTGGGTCATCGCCTC 59.681 60.000 0.00 0.00 43.55 4.70
2664 5878 0.398522 ATAGGTGGGTCATCGCCTCA 60.399 55.000 0.00 0.00 43.55 3.86
2665 5879 0.616395 TAGGTGGGTCATCGCCTCAA 60.616 55.000 0.00 0.00 43.55 3.02
2666 5880 1.002624 GGTGGGTCATCGCCTCAAA 60.003 57.895 0.00 0.00 34.64 2.69
2667 5881 0.394352 GGTGGGTCATCGCCTCAAAT 60.394 55.000 0.00 0.00 34.64 2.32
2668 5882 1.017387 GTGGGTCATCGCCTCAAATC 58.983 55.000 0.00 0.00 0.00 2.17
2669 5883 0.461870 TGGGTCATCGCCTCAAATCG 60.462 55.000 0.00 0.00 0.00 3.34
2670 5884 0.179084 GGGTCATCGCCTCAAATCGA 60.179 55.000 0.00 0.00 39.17 3.59
2671 5885 0.931005 GGTCATCGCCTCAAATCGAC 59.069 55.000 0.00 0.00 37.55 4.20
2672 5886 0.572590 GTCATCGCCTCAAATCGACG 59.427 55.000 0.00 0.00 37.55 5.12
2673 5887 0.527600 TCATCGCCTCAAATCGACGG 60.528 55.000 0.00 0.00 37.55 4.79
2674 5888 1.227263 ATCGCCTCAAATCGACGGG 60.227 57.895 0.00 0.00 37.55 5.28
2675 5889 3.564027 CGCCTCAAATCGACGGGC 61.564 66.667 0.00 0.00 39.43 6.13
2676 5890 2.435938 GCCTCAAATCGACGGGCA 60.436 61.111 5.78 0.00 42.08 5.36
2677 5891 2.750888 GCCTCAAATCGACGGGCAC 61.751 63.158 5.78 0.00 42.08 5.01
2678 5892 1.079127 CCTCAAATCGACGGGCACT 60.079 57.895 0.00 0.00 0.00 4.40
2679 5893 0.174845 CCTCAAATCGACGGGCACTA 59.825 55.000 0.00 0.00 0.00 2.74
2680 5894 1.202533 CCTCAAATCGACGGGCACTAT 60.203 52.381 0.00 0.00 0.00 2.12
2681 5895 2.035449 CCTCAAATCGACGGGCACTATA 59.965 50.000 0.00 0.00 0.00 1.31
2682 5896 3.309388 CTCAAATCGACGGGCACTATAG 58.691 50.000 0.00 0.00 0.00 1.31
2683 5897 1.792949 CAAATCGACGGGCACTATAGC 59.207 52.381 0.00 0.00 0.00 2.97
2684 5898 1.329256 AATCGACGGGCACTATAGCT 58.671 50.000 0.00 0.00 34.17 3.32
2685 5899 1.329256 ATCGACGGGCACTATAGCTT 58.671 50.000 0.00 0.00 34.17 3.74
2686 5900 1.971481 TCGACGGGCACTATAGCTTA 58.029 50.000 0.00 0.00 34.17 3.09
2687 5901 1.878088 TCGACGGGCACTATAGCTTAG 59.122 52.381 0.00 0.00 34.17 2.18
2688 5902 1.666311 CGACGGGCACTATAGCTTAGC 60.666 57.143 0.00 0.00 34.17 3.09
2689 5903 0.680061 ACGGGCACTATAGCTTAGCC 59.320 55.000 14.40 14.40 44.48 3.93
2690 5904 0.679505 CGGGCACTATAGCTTAGCCA 59.320 55.000 20.74 0.00 46.96 4.75
2691 5905 1.605712 CGGGCACTATAGCTTAGCCAC 60.606 57.143 20.74 12.70 46.96 5.01
2692 5906 1.694696 GGGCACTATAGCTTAGCCACT 59.305 52.381 20.74 0.00 46.96 4.00
2693 5907 2.104963 GGGCACTATAGCTTAGCCACTT 59.895 50.000 20.74 0.00 46.96 3.16
2694 5908 3.394719 GGCACTATAGCTTAGCCACTTC 58.605 50.000 16.67 0.00 44.59 3.01
2695 5909 3.394719 GCACTATAGCTTAGCCACTTCC 58.605 50.000 0.00 0.00 0.00 3.46
2696 5910 3.070302 GCACTATAGCTTAGCCACTTCCT 59.930 47.826 0.00 0.00 0.00 3.36
2697 5911 4.281182 GCACTATAGCTTAGCCACTTCCTA 59.719 45.833 0.00 0.00 0.00 2.94
2698 5912 5.221461 GCACTATAGCTTAGCCACTTCCTAA 60.221 44.000 0.00 0.00 0.00 2.69
2699 5913 6.685620 GCACTATAGCTTAGCCACTTCCTAAA 60.686 42.308 0.00 0.00 0.00 1.85
2700 5914 7.272978 CACTATAGCTTAGCCACTTCCTAAAA 58.727 38.462 0.00 0.00 0.00 1.52
2701 5915 7.224949 CACTATAGCTTAGCCACTTCCTAAAAC 59.775 40.741 0.00 0.00 0.00 2.43
2702 5916 4.367039 AGCTTAGCCACTTCCTAAAACA 57.633 40.909 0.00 0.00 0.00 2.83
2703 5917 4.072839 AGCTTAGCCACTTCCTAAAACAC 58.927 43.478 0.00 0.00 0.00 3.32
2704 5918 3.120304 GCTTAGCCACTTCCTAAAACACG 60.120 47.826 0.00 0.00 0.00 4.49
2705 5919 1.235724 AGCCACTTCCTAAAACACGC 58.764 50.000 0.00 0.00 0.00 5.34
2706 5920 0.240145 GCCACTTCCTAAAACACGCC 59.760 55.000 0.00 0.00 0.00 5.68
2707 5921 0.515564 CCACTTCCTAAAACACGCCG 59.484 55.000 0.00 0.00 0.00 6.46
2708 5922 1.504359 CACTTCCTAAAACACGCCGA 58.496 50.000 0.00 0.00 0.00 5.54
2709 5923 1.193874 CACTTCCTAAAACACGCCGAC 59.806 52.381 0.00 0.00 0.00 4.79
2710 5924 1.202557 ACTTCCTAAAACACGCCGACA 60.203 47.619 0.00 0.00 0.00 4.35
2711 5925 1.459592 CTTCCTAAAACACGCCGACAG 59.540 52.381 0.00 0.00 0.00 3.51
2712 5926 0.675083 TCCTAAAACACGCCGACAGA 59.325 50.000 0.00 0.00 0.00 3.41
2713 5927 1.274167 TCCTAAAACACGCCGACAGAT 59.726 47.619 0.00 0.00 0.00 2.90
2714 5928 2.492881 TCCTAAAACACGCCGACAGATA 59.507 45.455 0.00 0.00 0.00 1.98
2715 5929 3.056678 TCCTAAAACACGCCGACAGATAA 60.057 43.478 0.00 0.00 0.00 1.75
2716 5930 3.306166 CCTAAAACACGCCGACAGATAAG 59.694 47.826 0.00 0.00 0.00 1.73
2717 5931 2.736144 AAACACGCCGACAGATAAGA 57.264 45.000 0.00 0.00 0.00 2.10
2718 5932 2.961526 AACACGCCGACAGATAAGAT 57.038 45.000 0.00 0.00 0.00 2.40
2719 5933 2.493713 ACACGCCGACAGATAAGATC 57.506 50.000 0.00 0.00 0.00 2.75
2720 5934 1.067212 ACACGCCGACAGATAAGATCC 59.933 52.381 0.00 0.00 0.00 3.36
2721 5935 1.338337 CACGCCGACAGATAAGATCCT 59.662 52.381 0.00 0.00 0.00 3.24
2722 5936 1.609555 ACGCCGACAGATAAGATCCTC 59.390 52.381 0.00 0.00 0.00 3.71
2723 5937 1.400371 CGCCGACAGATAAGATCCTCG 60.400 57.143 0.00 0.00 32.59 4.63
2724 5938 1.880675 GCCGACAGATAAGATCCTCGA 59.119 52.381 5.96 0.00 33.89 4.04
2725 5939 2.490115 GCCGACAGATAAGATCCTCGAT 59.510 50.000 0.00 0.00 33.89 3.59
2726 5940 3.057174 GCCGACAGATAAGATCCTCGATT 60.057 47.826 0.00 0.00 33.89 3.34
2727 5941 4.480541 CCGACAGATAAGATCCTCGATTG 58.519 47.826 0.00 0.00 33.89 2.67
3026 6260 7.125792 TCCTTAATAAGCTCGAATCTTTCCT 57.874 36.000 5.12 0.00 0.00 3.36
3332 6575 3.909995 TCCTCTTCTTCCATCTTTGTCCA 59.090 43.478 0.00 0.00 0.00 4.02
3344 6587 5.982356 CATCTTTGTCCAGAGATGGAGTAA 58.018 41.667 16.22 0.00 42.82 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 82 2.591311 CGTCACAACCAACGACCGG 61.591 63.158 0.00 0.00 41.29 5.28
101 104 3.687102 ACGTGTGGATCCGGCGAA 61.687 61.111 23.08 0.00 0.00 4.70
122 125 6.721318 AGACTGCAAGGGAGTAAAAATGATA 58.279 36.000 0.00 0.00 39.30 2.15
154 159 1.396301 GCAAAGACGATGAGAAGCCTG 59.604 52.381 0.00 0.00 0.00 4.85
160 166 1.996292 CCGAAGCAAAGACGATGAGA 58.004 50.000 0.00 0.00 0.00 3.27
193 199 3.555956 TCGAAGAATCTTTATTCAGCGCC 59.444 43.478 2.29 0.00 43.44 6.53
378 385 2.124236 CGCTCCCGGACTACCTCT 60.124 66.667 0.73 0.00 0.00 3.69
543 550 0.472471 ACGAATCATACCGGGGCAAT 59.528 50.000 6.32 0.00 0.00 3.56
603 610 1.878088 CTCATATGCAGCTTTGCGGAT 59.122 47.619 0.00 0.00 37.69 4.18
659 669 4.787598 CAACCACCGAAGAAAAGAATGAG 58.212 43.478 0.00 0.00 0.00 2.90
850 891 7.640313 TGATATATTCTACCCGGACTCTACAT 58.360 38.462 0.73 0.00 0.00 2.29
934 4043 4.111016 CGCCAGCGTACGTCCTCA 62.111 66.667 17.90 0.00 34.35 3.86
951 4060 0.043310 GAGTTGTGTCGCGTTGTGTC 60.043 55.000 5.77 0.00 0.00 3.67
964 4073 3.057734 GGACTTGTTTCGATCGAGTTGT 58.942 45.455 18.54 13.28 30.65 3.32
1227 4336 2.180204 CACCCGCCGGATGACAATC 61.180 63.158 5.05 0.00 0.00 2.67
1317 4450 1.207089 CTCTGCGGGTTGATCTTGGTA 59.793 52.381 0.00 0.00 0.00 3.25
1650 4831 0.108207 GGTGGATGATGCCTCTCCAG 59.892 60.000 9.35 0.00 39.66 3.86
1704 4888 2.045926 GCCTGCTTCATGGACGGT 60.046 61.111 0.00 0.00 0.00 4.83
2298 5502 0.316204 CGACAAGGTGGTAGTTCCGT 59.684 55.000 0.00 0.00 39.52 4.69
2313 5517 2.962827 GAGAGCGTGGTCGTCGACA 61.963 63.158 25.64 10.15 39.49 4.35
2344 5548 2.639286 CGCCGCAAGCAGTTCTTT 59.361 55.556 0.00 0.00 44.04 2.52
2379 5589 1.954362 GCAGCATCTCGGACACCTCT 61.954 60.000 0.00 0.00 0.00 3.69
2453 5663 4.636648 TGTCGTTTGTTTTGCTTCTCCTTA 59.363 37.500 0.00 0.00 0.00 2.69
2481 5691 1.917273 TAGTTATGCCGTCGTTCTGC 58.083 50.000 0.00 0.00 0.00 4.26
2482 5692 3.508762 AGTTAGTTATGCCGTCGTTCTG 58.491 45.455 0.00 0.00 0.00 3.02
2483 5693 3.863142 AGTTAGTTATGCCGTCGTTCT 57.137 42.857 0.00 0.00 0.00 3.01
2526 5740 0.813610 CCGGTTGCAACACACAGAGA 60.814 55.000 29.55 0.00 0.00 3.10
2555 5769 9.221775 GATATTGAACCGCTAAAATTGTTACAG 57.778 33.333 0.00 0.00 0.00 2.74
2556 5770 8.185505 GGATATTGAACCGCTAAAATTGTTACA 58.814 33.333 0.00 0.00 0.00 2.41
2557 5771 8.185505 TGGATATTGAACCGCTAAAATTGTTAC 58.814 33.333 0.00 0.00 0.00 2.50
2570 5784 2.800544 GGACACGATGGATATTGAACCG 59.199 50.000 0.00 0.00 0.00 4.44
2582 5796 2.588877 GGGATGCCGGACACGATG 60.589 66.667 5.05 0.00 44.60 3.84
2591 5805 5.192927 ACAAATATATATGGTGGGATGCCG 58.807 41.667 0.00 0.00 0.00 5.69
2593 5807 9.632638 AATCTACAAATATATATGGTGGGATGC 57.367 33.333 9.46 0.00 0.00 3.91
2625 5839 8.831550 CACCTATCTAGCCTAAAATCAAAACTC 58.168 37.037 0.00 0.00 0.00 3.01
2628 5842 7.060421 CCCACCTATCTAGCCTAAAATCAAAA 58.940 38.462 0.00 0.00 0.00 2.44
2640 5854 1.067495 GCGATGACCCACCTATCTAGC 60.067 57.143 0.00 0.00 0.00 3.42
2650 5864 0.461870 CGATTTGAGGCGATGACCCA 60.462 55.000 0.00 0.00 0.00 4.51
2651 5865 0.179084 TCGATTTGAGGCGATGACCC 60.179 55.000 0.00 0.00 0.00 4.46
2652 5866 0.931005 GTCGATTTGAGGCGATGACC 59.069 55.000 0.00 0.00 38.91 4.02
2653 5867 0.572590 CGTCGATTTGAGGCGATGAC 59.427 55.000 0.00 0.00 44.03 3.06
2654 5868 0.527600 CCGTCGATTTGAGGCGATGA 60.528 55.000 0.00 0.00 44.03 2.92
2655 5869 1.490693 CCCGTCGATTTGAGGCGATG 61.491 60.000 0.00 0.00 39.29 3.84
2656 5870 1.227263 CCCGTCGATTTGAGGCGAT 60.227 57.895 0.00 0.00 39.29 4.58
2657 5871 2.183300 CCCGTCGATTTGAGGCGA 59.817 61.111 0.00 0.00 39.29 5.54
2658 5872 3.564027 GCCCGTCGATTTGAGGCG 61.564 66.667 0.00 0.00 33.18 5.52
2659 5873 2.435938 TGCCCGTCGATTTGAGGC 60.436 61.111 0.00 0.00 44.13 4.70
2660 5874 0.174845 TAGTGCCCGTCGATTTGAGG 59.825 55.000 0.00 0.00 0.00 3.86
2661 5875 2.225068 ATAGTGCCCGTCGATTTGAG 57.775 50.000 0.00 0.00 0.00 3.02
2662 5876 2.545113 GCTATAGTGCCCGTCGATTTGA 60.545 50.000 0.84 0.00 0.00 2.69
2663 5877 1.792949 GCTATAGTGCCCGTCGATTTG 59.207 52.381 0.84 0.00 0.00 2.32
2664 5878 1.687123 AGCTATAGTGCCCGTCGATTT 59.313 47.619 0.84 0.00 0.00 2.17
2665 5879 1.329256 AGCTATAGTGCCCGTCGATT 58.671 50.000 0.84 0.00 0.00 3.34
2666 5880 1.329256 AAGCTATAGTGCCCGTCGAT 58.671 50.000 0.84 0.00 0.00 3.59
2667 5881 1.878088 CTAAGCTATAGTGCCCGTCGA 59.122 52.381 0.84 0.00 0.00 4.20
2668 5882 1.666311 GCTAAGCTATAGTGCCCGTCG 60.666 57.143 0.84 0.00 0.00 5.12
2669 5883 1.336980 GGCTAAGCTATAGTGCCCGTC 60.337 57.143 13.47 0.00 37.81 4.79
2670 5884 0.680061 GGCTAAGCTATAGTGCCCGT 59.320 55.000 13.47 0.00 37.81 5.28
2671 5885 0.679505 TGGCTAAGCTATAGTGCCCG 59.320 55.000 18.41 1.65 42.62 6.13
2672 5886 1.694696 AGTGGCTAAGCTATAGTGCCC 59.305 52.381 18.41 12.76 42.62 5.36
2673 5887 3.394719 GAAGTGGCTAAGCTATAGTGCC 58.605 50.000 16.01 16.01 43.49 5.01
2674 5888 3.070302 AGGAAGTGGCTAAGCTATAGTGC 59.930 47.826 0.84 1.67 0.00 4.40
2675 5889 4.946478 AGGAAGTGGCTAAGCTATAGTG 57.054 45.455 0.84 0.00 0.00 2.74
2676 5890 7.093024 TGTTTTAGGAAGTGGCTAAGCTATAGT 60.093 37.037 0.84 0.00 0.00 2.12
2677 5891 7.224949 GTGTTTTAGGAAGTGGCTAAGCTATAG 59.775 40.741 0.00 0.00 0.00 1.31
2678 5892 7.046033 GTGTTTTAGGAAGTGGCTAAGCTATA 58.954 38.462 0.00 0.00 0.00 1.31
2679 5893 5.880887 GTGTTTTAGGAAGTGGCTAAGCTAT 59.119 40.000 0.00 0.00 0.00 2.97
2680 5894 5.243207 GTGTTTTAGGAAGTGGCTAAGCTA 58.757 41.667 0.00 0.00 0.00 3.32
2681 5895 4.072839 GTGTTTTAGGAAGTGGCTAAGCT 58.927 43.478 0.00 0.00 0.00 3.74
2682 5896 3.120304 CGTGTTTTAGGAAGTGGCTAAGC 60.120 47.826 0.00 0.00 0.00 3.09
2683 5897 3.120304 GCGTGTTTTAGGAAGTGGCTAAG 60.120 47.826 0.00 0.00 0.00 2.18
2684 5898 2.809696 GCGTGTTTTAGGAAGTGGCTAA 59.190 45.455 0.00 0.00 0.00 3.09
2685 5899 2.419667 GCGTGTTTTAGGAAGTGGCTA 58.580 47.619 0.00 0.00 0.00 3.93
2686 5900 1.235724 GCGTGTTTTAGGAAGTGGCT 58.764 50.000 0.00 0.00 0.00 4.75
2687 5901 0.240145 GGCGTGTTTTAGGAAGTGGC 59.760 55.000 0.00 0.00 0.00 5.01
2688 5902 0.515564 CGGCGTGTTTTAGGAAGTGG 59.484 55.000 0.00 0.00 0.00 4.00
2689 5903 1.193874 GTCGGCGTGTTTTAGGAAGTG 59.806 52.381 6.85 0.00 0.00 3.16
2690 5904 1.202557 TGTCGGCGTGTTTTAGGAAGT 60.203 47.619 6.85 0.00 0.00 3.01
2691 5905 1.459592 CTGTCGGCGTGTTTTAGGAAG 59.540 52.381 6.85 0.00 0.00 3.46
2692 5906 1.068895 TCTGTCGGCGTGTTTTAGGAA 59.931 47.619 6.85 0.00 0.00 3.36
2693 5907 0.675083 TCTGTCGGCGTGTTTTAGGA 59.325 50.000 6.85 0.00 0.00 2.94
2694 5908 1.722011 ATCTGTCGGCGTGTTTTAGG 58.278 50.000 6.85 0.00 0.00 2.69
2695 5909 4.171005 TCTTATCTGTCGGCGTGTTTTAG 58.829 43.478 6.85 0.00 0.00 1.85
2696 5910 4.177165 TCTTATCTGTCGGCGTGTTTTA 57.823 40.909 6.85 0.00 0.00 1.52
2697 5911 3.034721 TCTTATCTGTCGGCGTGTTTT 57.965 42.857 6.85 0.00 0.00 2.43
2698 5912 2.736144 TCTTATCTGTCGGCGTGTTT 57.264 45.000 6.85 0.00 0.00 2.83
2699 5913 2.481449 GGATCTTATCTGTCGGCGTGTT 60.481 50.000 6.85 0.00 0.00 3.32
2700 5914 1.067212 GGATCTTATCTGTCGGCGTGT 59.933 52.381 6.85 0.00 0.00 4.49
2701 5915 1.338337 AGGATCTTATCTGTCGGCGTG 59.662 52.381 6.85 0.00 0.00 5.34
2702 5916 1.609555 GAGGATCTTATCTGTCGGCGT 59.390 52.381 6.85 0.00 0.00 5.68
2703 5917 1.400371 CGAGGATCTTATCTGTCGGCG 60.400 57.143 0.00 0.00 34.37 6.46
2704 5918 1.880675 TCGAGGATCTTATCTGTCGGC 59.119 52.381 0.00 0.00 36.79 5.54
2705 5919 4.480541 CAATCGAGGATCTTATCTGTCGG 58.519 47.826 0.00 0.00 36.79 4.79
2706 5920 4.480541 CCAATCGAGGATCTTATCTGTCG 58.519 47.826 0.00 0.00 37.19 4.35
2707 5921 4.241681 GCCAATCGAGGATCTTATCTGTC 58.758 47.826 0.00 0.00 0.00 3.51
2708 5922 3.643320 TGCCAATCGAGGATCTTATCTGT 59.357 43.478 0.00 0.00 0.00 3.41
2709 5923 3.993081 GTGCCAATCGAGGATCTTATCTG 59.007 47.826 0.00 0.00 0.00 2.90
2710 5924 3.643320 TGTGCCAATCGAGGATCTTATCT 59.357 43.478 0.00 0.00 0.00 1.98
2711 5925 3.995199 TGTGCCAATCGAGGATCTTATC 58.005 45.455 0.00 0.00 0.00 1.75
2712 5926 4.101585 TCTTGTGCCAATCGAGGATCTTAT 59.898 41.667 0.00 0.00 0.00 1.73
2713 5927 3.450817 TCTTGTGCCAATCGAGGATCTTA 59.549 43.478 0.00 0.00 0.00 2.10
2714 5928 2.237143 TCTTGTGCCAATCGAGGATCTT 59.763 45.455 0.00 0.00 0.00 2.40
2715 5929 1.833630 TCTTGTGCCAATCGAGGATCT 59.166 47.619 0.00 0.00 0.00 2.75
2716 5930 2.315925 TCTTGTGCCAATCGAGGATC 57.684 50.000 0.00 0.00 0.00 3.36
2717 5931 2.787473 TTCTTGTGCCAATCGAGGAT 57.213 45.000 0.00 0.00 0.00 3.24
2718 5932 2.559698 TTTCTTGTGCCAATCGAGGA 57.440 45.000 0.00 0.00 0.00 3.71
2719 5933 2.554032 ACTTTTCTTGTGCCAATCGAGG 59.446 45.455 0.00 0.00 0.00 4.63
2720 5934 3.003689 ACACTTTTCTTGTGCCAATCGAG 59.996 43.478 0.00 0.00 38.86 4.04
2721 5935 2.948979 ACACTTTTCTTGTGCCAATCGA 59.051 40.909 0.00 0.00 38.86 3.59
2722 5936 3.300009 GACACTTTTCTTGTGCCAATCG 58.700 45.455 0.00 0.00 38.86 3.34
2723 5937 3.300009 CGACACTTTTCTTGTGCCAATC 58.700 45.455 0.00 0.00 38.86 2.67
2724 5938 2.543653 GCGACACTTTTCTTGTGCCAAT 60.544 45.455 0.00 0.00 38.86 3.16
2725 5939 1.202245 GCGACACTTTTCTTGTGCCAA 60.202 47.619 0.00 0.00 38.86 4.52
2726 5940 0.380378 GCGACACTTTTCTTGTGCCA 59.620 50.000 0.00 0.00 38.86 4.92
2727 5941 0.317854 GGCGACACTTTTCTTGTGCC 60.318 55.000 0.00 0.00 38.86 5.01
3203 6437 1.415672 TTCGGCCAGAAAGGTCACCT 61.416 55.000 2.24 0.00 44.49 4.00
3332 6575 1.689273 GACCGCCATTACTCCATCTCT 59.311 52.381 0.00 0.00 0.00 3.10
3344 6587 3.861797 GGATCACCGGACCGCCAT 61.862 66.667 9.46 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.