Multiple sequence alignment - TraesCS2A01G017100

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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 TraesCS2A01G017100 chr2A 100.000 4444 0 0 1 4444 7918298 7922741 0.000000e+00 8207.0
1 TraesCS2A01G017100 chr2A 84.705 1373 159 28 1137 2482 8182478 8181130 0.000000e+00 1325.0
2 TraesCS2A01G017100 chr2A 75.772 1490 267 64 980 2422 8314965 8313523 0.000000e+00 665.0
3 TraesCS2A01G017100 chr2A 86.025 551 46 9 7 527 113815947 113816496 3.000000e-156 562.0
4 TraesCS2A01G017100 chr2A 82.305 616 68 20 3245 3835 8180854 8180255 3.090000e-136 496.0
5 TraesCS2A01G017100 chr2A 82.213 506 67 16 2752 3248 8369577 8369086 8.890000e-112 414.0
6 TraesCS2A01G017100 chr2A 90.909 231 17 4 3020 3247 8181051 8180822 1.550000e-79 307.0
7 TraesCS2A01G017100 chr2A 84.314 255 19 13 2752 2999 7808188 7808428 3.460000e-56 230.0
8 TraesCS2A01G017100 chr2A 85.116 215 22 4 3042 3247 7808875 7809088 1.250000e-50 211.0
9 TraesCS2A01G017100 chr2A 94.444 108 4 1 2492 2597 8181333 8181226 9.890000e-37 165.0
10 TraesCS2A01G017100 chr2A 75.439 228 26 15 853 1056 8182756 8182535 2.850000e-12 84.2
11 TraesCS2A01G017100 chr2A 88.710 62 3 3 907 968 8045293 8045350 6.170000e-09 73.1
12 TraesCS2A01G017100 chr3D 96.626 3705 82 18 773 4444 563859320 563863014 0.000000e+00 6109.0
13 TraesCS2A01G017100 chr3D 85.932 590 47 10 150 708 402495217 402494633 8.230000e-167 597.0
14 TraesCS2A01G017100 chr3D 85.882 595 45 16 150 713 420047578 420048164 8.230000e-167 597.0
15 TraesCS2A01G017100 chr3D 84.837 521 40 16 223 712 547039880 547040392 5.170000e-134 488.0
16 TraesCS2A01G017100 chr3D 92.836 335 20 2 7 338 278980211 278980544 2.400000e-132 483.0
17 TraesCS2A01G017100 chr3D 94.479 163 7 1 2593 2753 87925999 87926161 2.650000e-62 250.0
18 TraesCS2A01G017100 chr3D 92.593 108 6 1 2492 2597 563860850 563860957 2.140000e-33 154.0
19 TraesCS2A01G017100 chr7A 85.590 1374 153 30 1253 2597 466508137 466509494 0.000000e+00 1399.0
20 TraesCS2A01G017100 chr7A 82.872 397 28 22 2876 3247 466509686 466510067 1.990000e-83 320.0
21 TraesCS2A01G017100 chr7A 81.527 406 44 19 3245 3641 466510035 466510418 5.580000e-79 305.0
22 TraesCS2A01G017100 chr7A 78.936 470 65 16 1965 2422 466492005 466492452 5.620000e-74 289.0
23 TraesCS2A01G017100 chr7A 92.670 191 13 1 2760 2950 466509499 466509688 1.570000e-69 274.0
24 TraesCS2A01G017100 chr7A 89.573 211 17 3 2276 2483 466509383 466509591 3.410000e-66 263.0
25 TraesCS2A01G017100 chr7A 93.578 109 5 1 2492 2598 466509178 466509286 1.280000e-35 161.0
26 TraesCS2A01G017100 chr7A 83.465 127 3 8 793 902 466507556 466507681 7.860000e-18 102.0
27 TraesCS2A01G017100 chr2B 84.895 1238 140 25 1179 2389 70881961 70880744 0.000000e+00 1206.0
28 TraesCS2A01G017100 chr2B 81.164 945 111 37 2745 3668 12076257 12075359 0.000000e+00 697.0
29 TraesCS2A01G017100 chr2B 74.606 1650 278 76 907 2486 11984478 11986056 2.960000e-166 595.0
30 TraesCS2A01G017100 chr2B 82.249 507 65 18 2752 3248 12025631 12025140 8.890000e-112 414.0
31 TraesCS2A01G017100 chr2B 84.406 404 26 10 2760 3141 70880446 70880058 3.270000e-96 363.0
32 TraesCS2A01G017100 chr2B 77.778 621 97 27 1880 2479 12026137 12025537 1.180000e-90 344.0
33 TraesCS2A01G017100 chr2B 90.187 214 16 3 2276 2486 70880562 70880351 1.570000e-69 274.0
34 TraesCS2A01G017100 chr2B 85.271 258 28 6 2752 3003 11985947 11986200 1.590000e-64 257.0
35 TraesCS2A01G017100 chr2B 85.253 217 23 7 2386 2597 70880663 70880451 9.680000e-52 215.0
36 TraesCS2A01G017100 chr2B 84.946 186 24 4 2597 2779 775119314 775119130 7.590000e-43 185.0
37 TraesCS2A01G017100 chr2B 92.913 127 5 3 2492 2616 70880851 70880727 9.820000e-42 182.0
38 TraesCS2A01G017100 chr2B 77.188 320 38 21 747 1041 12027270 12026961 2.140000e-33 154.0
39 TraesCS2A01G017100 chr2B 90.000 100 4 2 755 848 12077947 12077848 1.680000e-24 124.0
40 TraesCS2A01G017100 chr2B 85.849 106 7 5 851 948 70882806 70882701 6.080000e-19 106.0
41 TraesCS2A01G017100 chr2B 80.769 130 18 5 916 1041 12077729 12077603 1.320000e-15 95.3
42 TraesCS2A01G017100 chr2B 95.833 48 1 1 861 907 12077811 12077764 4.770000e-10 76.8
43 TraesCS2A01G017100 chr2D 88.917 803 74 8 1806 2597 8928474 8929272 0.000000e+00 976.0
44 TraesCS2A01G017100 chr2D 76.324 1681 292 70 861 2482 8888810 8890443 0.000000e+00 802.0
45 TraesCS2A01G017100 chr2D 86.486 592 44 16 150 712 549981677 549982261 6.320000e-173 617.0
46 TraesCS2A01G017100 chr2D 85.149 505 50 19 2760 3247 8929277 8929773 1.110000e-135 494.0
47 TraesCS2A01G017100 chr2D 76.520 1069 152 59 780 1814 8920019 8921022 3.990000e-135 492.0
48 TraesCS2A01G017100 chr2D 92.169 332 25 1 7 338 340692033 340691703 6.730000e-128 468.0
49 TraesCS2A01G017100 chr2D 82.738 504 66 14 2752 3248 8717550 8718039 3.180000e-116 429.0
50 TraesCS2A01G017100 chr2D 83.879 428 51 13 2752 3169 8890345 8890764 4.170000e-105 392.0
51 TraesCS2A01G017100 chr2D 78.537 615 102 19 1881 2483 8717052 8717648 1.170000e-100 377.0
52 TraesCS2A01G017100 chr2D 89.450 218 17 4 2276 2489 8929161 8929376 2.040000e-68 270.0
53 TraesCS2A01G017100 chr2D 80.453 353 49 14 1150 1492 8716273 8716615 7.380000e-63 252.0
54 TraesCS2A01G017100 chr2D 81.858 226 17 8 828 1038 8715963 8716179 7.640000e-38 169.0
55 TraesCS2A01G017100 chr2D 94.444 108 4 1 2492 2597 8928956 8929063 9.890000e-37 165.0
56 TraesCS2A01G017100 chr2D 92.941 85 6 0 3620 3704 8930265 8930349 1.680000e-24 124.0
57 TraesCS2A01G017100 chr4D 85.714 735 59 19 8 708 439179104 439179826 0.000000e+00 734.0
58 TraesCS2A01G017100 chr7D 87.500 656 45 6 8 630 554900035 554899384 0.000000e+00 723.0
59 TraesCS2A01G017100 chr7D 91.940 335 23 2 7 338 523541835 523542168 2.420000e-127 466.0
60 TraesCS2A01G017100 chr7D 84.653 202 25 6 2594 2790 453283502 453283702 3.510000e-46 196.0
61 TraesCS2A01G017100 chr7D 82.723 191 27 5 2594 2779 124026642 124026831 9.890000e-37 165.0
62 TraesCS2A01G017100 chr3B 89.077 531 50 7 135 661 683831338 683831864 0.000000e+00 652.0
63 TraesCS2A01G017100 chr3B 91.954 174 11 2 2594 2765 43276237 43276065 1.600000e-59 241.0
64 TraesCS2A01G017100 chr6D 83.378 740 80 25 7 712 38628042 38628772 0.000000e+00 645.0
65 TraesCS2A01G017100 chr5A 86.027 594 44 13 150 712 580928379 580927794 6.360000e-168 601.0
66 TraesCS2A01G017100 chr5A 95.092 163 6 1 2594 2754 653299601 653299439 5.700000e-64 255.0
67 TraesCS2A01G017100 chr5A 94.512 164 7 1 2592 2753 320214242 320214405 7.380000e-63 252.0
68 TraesCS2A01G017100 chr5A 81.592 201 23 9 2589 2779 527485924 527485728 2.140000e-33 154.0
69 TraesCS2A01G017100 chr1D 85.497 593 48 13 150 712 469096249 469095665 6.410000e-163 584.0
70 TraesCS2A01G017100 chr1D 86.842 380 38 7 338 712 433908081 433907709 8.890000e-112 414.0
71 TraesCS2A01G017100 chr3A 84.706 595 52 14 150 713 123047422 123046836 3.880000e-155 558.0
72 TraesCS2A01G017100 chr4A 91.789 341 25 3 7 346 144026967 144026629 5.200000e-129 472.0
73 TraesCS2A01G017100 chr5D 95.031 161 8 0 2593 2753 150835465 150835305 2.050000e-63 254.0
74 TraesCS2A01G017100 chr5D 94.479 163 7 1 2594 2754 150835568 150835730 2.650000e-62 250.0
75 TraesCS2A01G017100 chr5D 85.276 163 19 4 2593 2753 66666431 66666590 3.560000e-36 163.0
76 TraesCS2A01G017100 chr1B 93.567 171 9 1 2594 2762 436689151 436688981 2.050000e-63 254.0
77 TraesCS2A01G017100 chr1B 86.458 192 17 7 2594 2778 266806096 266805907 7.540000e-48 202.0
78 TraesCS2A01G017100 chr4B 93.976 166 8 1 2593 2756 606916762 606916927 2.650000e-62 250.0
79 TraesCS2A01G017100 chr5B 85.128 195 17 10 2594 2778 182734474 182734282 5.870000e-44 189.0
80 TraesCS2A01G017100 chr7B 83.168 202 23 9 2593 2784 573132306 573132106 1.640000e-39 174.0


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 TraesCS2A01G017100 chr2A 7918298 7922741 4443 False 8207.000000 8207 100.000000 1 4444 1 chr2A.!!$F1 4443
1 TraesCS2A01G017100 chr2A 8313523 8314965 1442 True 665.000000 665 75.772000 980 2422 1 chr2A.!!$R1 1442
2 TraesCS2A01G017100 chr2A 113815947 113816496 549 False 562.000000 562 86.025000 7 527 1 chr2A.!!$F3 520
3 TraesCS2A01G017100 chr2A 8180255 8182756 2501 True 475.440000 1325 85.560400 853 3835 5 chr2A.!!$R3 2982
4 TraesCS2A01G017100 chr2A 7808188 7809088 900 False 220.500000 230 84.715000 2752 3247 2 chr2A.!!$F4 495
5 TraesCS2A01G017100 chr3D 563859320 563863014 3694 False 3131.500000 6109 94.609500 773 4444 2 chr3D.!!$F5 3671
6 TraesCS2A01G017100 chr3D 402494633 402495217 584 True 597.000000 597 85.932000 150 708 1 chr3D.!!$R1 558
7 TraesCS2A01G017100 chr3D 420047578 420048164 586 False 597.000000 597 85.882000 150 713 1 chr3D.!!$F3 563
8 TraesCS2A01G017100 chr3D 547039880 547040392 512 False 488.000000 488 84.837000 223 712 1 chr3D.!!$F4 489
9 TraesCS2A01G017100 chr7A 466507556 466510418 2862 False 403.428571 1399 87.039286 793 3641 7 chr7A.!!$F2 2848
10 TraesCS2A01G017100 chr2B 11984478 11986200 1722 False 426.000000 595 79.938500 907 3003 2 chr2B.!!$F1 2096
11 TraesCS2A01G017100 chr2B 70880058 70882806 2748 True 391.000000 1206 87.250500 851 3141 6 chr2B.!!$R4 2290
12 TraesCS2A01G017100 chr2B 12025140 12027270 2130 True 304.000000 414 79.071667 747 3248 3 chr2B.!!$R2 2501
13 TraesCS2A01G017100 chr2B 12075359 12077947 2588 True 248.275000 697 86.941500 755 3668 4 chr2B.!!$R3 2913
14 TraesCS2A01G017100 chr2D 549981677 549982261 584 False 617.000000 617 86.486000 150 712 1 chr2D.!!$F2 562
15 TraesCS2A01G017100 chr2D 8888810 8890764 1954 False 597.000000 802 80.101500 861 3169 2 chr2D.!!$F4 2308
16 TraesCS2A01G017100 chr2D 8920019 8921022 1003 False 492.000000 492 76.520000 780 1814 1 chr2D.!!$F1 1034
17 TraesCS2A01G017100 chr2D 8928474 8930349 1875 False 405.800000 976 90.180200 1806 3704 5 chr2D.!!$F5 1898
18 TraesCS2A01G017100 chr2D 8715963 8718039 2076 False 306.750000 429 80.896500 828 3248 4 chr2D.!!$F3 2420
19 TraesCS2A01G017100 chr4D 439179104 439179826 722 False 734.000000 734 85.714000 8 708 1 chr4D.!!$F1 700
20 TraesCS2A01G017100 chr7D 554899384 554900035 651 True 723.000000 723 87.500000 8 630 1 chr7D.!!$R1 622
21 TraesCS2A01G017100 chr3B 683831338 683831864 526 False 652.000000 652 89.077000 135 661 1 chr3B.!!$F1 526
22 TraesCS2A01G017100 chr6D 38628042 38628772 730 False 645.000000 645 83.378000 7 712 1 chr6D.!!$F1 705
23 TraesCS2A01G017100 chr5A 580927794 580928379 585 True 601.000000 601 86.027000 150 712 1 chr5A.!!$R2 562
24 TraesCS2A01G017100 chr1D 469095665 469096249 584 True 584.000000 584 85.497000 150 712 1 chr1D.!!$R2 562
25 TraesCS2A01G017100 chr3A 123046836 123047422 586 True 558.000000 558 84.706000 150 713 1 chr3A.!!$R1 563

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
917 1075 0.031414 TCCTCCACCTAACCCTAGCC 60.031 60.0 0.00 0.0 0.00 3.93 F
1504 2374 0.037734 TGAGCTCGTCTGGGTCTGTA 59.962 55.0 9.64 0.0 33.06 2.74 F
2087 3077 1.342082 CGACTAGTGTTCAACGCCCG 61.342 60.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2822 0.729140 GGGCTCGCGTTCAACAAATG 60.729 55.000 5.77 0.0 0.0 2.32 R
2973 4321 1.737793 GGGGTGAAGCTAATGACAACG 59.262 52.381 0.00 0.0 0.0 4.10 R
3903 5869 0.682209 ATCCAGCCATGCCACAGAAC 60.682 55.000 0.00 0.0 0.0 3.01 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
148 152 0.532573 GAGGCTTGAGATGGACGTGA 59.467 55.000 0.00 0.00 0.00 4.35
232 236 2.278792 TCGCGAGCATGATGACCG 60.279 61.111 3.71 0.00 0.00 4.79
254 258 1.673168 GGTGGAGATCATGAAGGTGC 58.327 55.000 0.00 0.00 0.00 5.01
264 268 3.753815 TCATGAAGGTGCATCTCAACAA 58.246 40.909 0.00 0.00 33.90 2.83
330 334 0.732880 ATGCTCAAGTTCGACGACGG 60.733 55.000 7.55 0.00 40.21 4.79
387 420 2.048597 GCCGTGATGACGTGGTCA 60.049 61.111 3.53 0.38 46.90 4.02
479 518 3.286353 TGTGGTGATGTTTTCTGAAGCA 58.714 40.909 0.00 0.00 0.00 3.91
527 569 1.450848 CAGCATGAGACATGGCCGT 60.451 57.895 12.56 0.00 39.69 5.68
586 638 3.008594 AGTGTGGACATAAAATGGGTCGA 59.991 43.478 0.00 0.00 32.39 4.20
587 639 3.945285 GTGTGGACATAAAATGGGTCGAT 59.055 43.478 0.00 0.00 32.39 3.59
630 682 3.566322 CCAAATACAAAACTGGACGGACA 59.434 43.478 0.00 0.00 0.00 4.02
687 740 2.686816 GGACAAATGCACCGTCCGG 61.687 63.158 13.53 3.76 39.86 5.14
708 763 1.198094 TGATCGGCCCTTGGAGTTGA 61.198 55.000 0.00 0.00 0.00 3.18
713 768 0.394899 GGCCCTTGGAGTTGATCTGG 60.395 60.000 0.00 0.00 0.00 3.86
714 769 1.034292 GCCCTTGGAGTTGATCTGGC 61.034 60.000 0.00 0.00 0.00 4.85
715 770 0.329261 CCCTTGGAGTTGATCTGGCA 59.671 55.000 0.00 0.00 0.00 4.92
716 771 1.681166 CCCTTGGAGTTGATCTGGCAG 60.681 57.143 8.58 8.58 0.00 4.85
717 772 1.004044 CCTTGGAGTTGATCTGGCAGT 59.996 52.381 15.27 1.47 0.00 4.40
718 773 2.082231 CTTGGAGTTGATCTGGCAGTG 58.918 52.381 15.27 0.00 0.00 3.66
719 774 1.059098 TGGAGTTGATCTGGCAGTGT 58.941 50.000 15.27 4.54 0.00 3.55
720 775 1.271001 TGGAGTTGATCTGGCAGTGTG 60.271 52.381 15.27 0.00 0.00 3.82
721 776 1.002430 GGAGTTGATCTGGCAGTGTGA 59.998 52.381 15.27 0.00 0.00 3.58
722 777 2.550855 GGAGTTGATCTGGCAGTGTGAA 60.551 50.000 15.27 2.49 0.00 3.18
723 778 3.141398 GAGTTGATCTGGCAGTGTGAAA 58.859 45.455 15.27 0.90 0.00 2.69
724 779 3.554934 AGTTGATCTGGCAGTGTGAAAA 58.445 40.909 15.27 0.00 0.00 2.29
725 780 3.953612 AGTTGATCTGGCAGTGTGAAAAA 59.046 39.130 15.27 0.00 0.00 1.94
726 781 4.037208 AGTTGATCTGGCAGTGTGAAAAAG 59.963 41.667 15.27 0.00 0.00 2.27
727 782 2.294233 TGATCTGGCAGTGTGAAAAAGC 59.706 45.455 15.27 0.00 0.00 3.51
728 783 0.662619 TCTGGCAGTGTGAAAAAGCG 59.337 50.000 15.27 0.00 0.00 4.68
729 784 0.662619 CTGGCAGTGTGAAAAAGCGA 59.337 50.000 6.28 0.00 0.00 4.93
730 785 1.065401 CTGGCAGTGTGAAAAAGCGAA 59.935 47.619 6.28 0.00 0.00 4.70
731 786 1.065401 TGGCAGTGTGAAAAAGCGAAG 59.935 47.619 0.00 0.00 0.00 3.79
744 799 4.139420 CGAAGCGCCGAAGCACAG 62.139 66.667 2.29 0.00 39.83 3.66
745 800 2.738521 GAAGCGCCGAAGCACAGA 60.739 61.111 2.29 0.00 39.83 3.41
751 806 2.125912 CCGAAGCACAGACCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
917 1075 0.031414 TCCTCCACCTAACCCTAGCC 60.031 60.000 0.00 0.00 0.00 3.93
918 1076 1.400530 CCTCCACCTAACCCTAGCCG 61.401 65.000 0.00 0.00 0.00 5.52
919 1077 2.029307 CTCCACCTAACCCTAGCCGC 62.029 65.000 0.00 0.00 0.00 6.53
920 1078 2.064581 CCACCTAACCCTAGCCGCT 61.065 63.158 0.00 0.00 0.00 5.52
977 1598 3.501385 CCTCCACCAAACCCTAATCCAAA 60.501 47.826 0.00 0.00 0.00 3.28
978 1599 3.763897 CTCCACCAAACCCTAATCCAAAG 59.236 47.826 0.00 0.00 0.00 2.77
1075 1794 1.749033 GGGATCTACGAAGGGCCAG 59.251 63.158 6.18 0.00 0.00 4.85
1107 1832 0.393132 GGGGACTACCAGCAAGAAGC 60.393 60.000 0.00 0.00 42.91 3.86
1133 1864 2.211468 GAGGGCCCGGGAAAGTTGAT 62.211 60.000 29.31 0.00 0.00 2.57
1135 1866 1.320344 GGGCCCGGGAAAGTTGATTC 61.320 60.000 29.31 0.76 0.00 2.52
1167 1898 3.674997 GGAGTACCTGCAGACATTCAAA 58.325 45.455 17.39 0.00 0.00 2.69
1418 2279 2.125512 CGGCACCTGCAGGACTAC 60.126 66.667 39.19 22.43 44.36 2.73
1430 2291 0.550147 AGGACTACAGCCATGGGGTT 60.550 55.000 15.13 0.00 36.17 4.11
1504 2374 0.037734 TGAGCTCGTCTGGGTCTGTA 59.962 55.000 9.64 0.00 33.06 2.74
1838 2822 3.371285 GTCAAGTTCCTCGCCTTCAATAC 59.629 47.826 0.00 0.00 0.00 1.89
1907 2891 2.433318 GTCGCCTGACCACTCAGC 60.433 66.667 0.00 0.00 42.55 4.26
2057 3041 4.982916 CCTAGTCGTAAATGATACCAGTGC 59.017 45.833 0.00 0.00 0.00 4.40
2082 3072 2.314122 GGTCGTCGACTAGTGTTCAAC 58.686 52.381 23.69 0.55 32.47 3.18
2087 3077 1.342082 CGACTAGTGTTCAACGCCCG 61.342 60.000 0.00 0.00 0.00 6.13
2451 3468 8.093927 TGTTCAACAGTAGATGTGTGATATTGA 58.906 33.333 0.00 0.00 43.00 2.57
2460 3477 9.283420 GTAGATGTGTGATATTGATACTCATCG 57.717 37.037 0.00 0.00 44.07 3.84
2894 4148 3.071602 CCCCTTGTCATATCAGTACCCAG 59.928 52.174 0.00 0.00 0.00 4.45
2973 4321 9.260002 CTTTTCTTTTCCTCTGATAGAGATAGC 57.740 37.037 7.39 0.00 45.07 2.97
3029 4779 1.425066 TGAAGACCTGGGCATTCAGTT 59.575 47.619 0.47 0.00 33.14 3.16
3205 4983 2.349438 CCTTGACACAATGGTCGTTTCG 60.349 50.000 0.00 0.00 40.72 3.46
3426 5205 5.218139 CAGACTTCTCTGTTTCATTTTGCC 58.782 41.667 0.00 0.00 39.43 4.52
3678 5643 4.439305 TTGGATTGTAACTTGCATCAGC 57.561 40.909 0.00 0.00 42.57 4.26
3723 5689 8.792633 TCCTACTGGTTTGATTTAGAAACAATG 58.207 33.333 0.00 0.00 35.40 2.82
3903 5869 7.201635 GGCATTGCCTTTTCTTGGTTATATTTG 60.202 37.037 20.66 0.00 46.69 2.32
4183 6149 9.653287 CATTTGTATTTAGTGTGGACTAGAGAA 57.347 33.333 0.00 0.00 36.03 2.87
4219 6185 3.644265 GGAGGCCCCAAAAACTTTTTAGA 59.356 43.478 0.00 0.00 34.14 2.10
4220 6186 4.101898 GGAGGCCCCAAAAACTTTTTAGAA 59.898 41.667 0.00 0.00 34.14 2.10
4255 6221 1.424638 CCCTATCTTCCATGGTCGGT 58.575 55.000 12.58 2.75 0.00 4.69
4302 6268 2.584391 GGCAGGGGTCGTGAGTCTT 61.584 63.158 0.00 0.00 0.00 3.01
4347 6313 2.764547 GGAGCTAGGCGGGGAAGT 60.765 66.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.425422 GATGCCGCATCCTTGTCC 58.575 61.111 20.86 0.00 35.07 4.02
107 111 3.950395 CCTCCTTTGGATCTCCATGAAAC 59.050 47.826 0.00 0.00 46.97 2.78
148 152 1.920610 AGCATCTTGGCTTGCTTCTT 58.079 45.000 0.00 0.00 46.71 2.52
232 236 0.475906 CCTTCATGATCTCCACCCCC 59.524 60.000 0.00 0.00 0.00 5.40
254 258 0.163788 GGCGACACGTTGTTGAGATG 59.836 55.000 8.89 0.00 33.58 2.90
264 268 1.006102 CTCTTCCTTGGCGACACGT 60.006 57.895 0.00 0.00 42.67 4.49
330 334 1.302033 CCTGCCGCCATAGATCACC 60.302 63.158 0.00 0.00 0.00 4.02
374 407 2.900716 TGAGTTTGACCACGTCATCA 57.099 45.000 0.00 0.00 42.40 3.07
454 488 5.679638 GCTTCAGAAAACATCACCACAGTTT 60.680 40.000 0.00 0.00 37.08 2.66
510 549 1.028330 CAACGGCCATGTCTCATGCT 61.028 55.000 2.24 0.00 0.00 3.79
527 569 1.314534 CCCGCAACTGATCATGCCAA 61.315 55.000 14.19 0.00 39.39 4.52
556 607 7.040062 CCCATTTTATGTCCACACTCAACTTAA 60.040 37.037 0.00 0.00 0.00 1.85
557 608 6.432783 CCCATTTTATGTCCACACTCAACTTA 59.567 38.462 0.00 0.00 0.00 2.24
664 717 3.560826 CGGTGCATTTGTCCGTTTT 57.439 47.368 4.61 0.00 39.51 2.43
687 740 0.322546 AACTCCAAGGGCCGATCAAC 60.323 55.000 0.00 0.00 0.00 3.18
692 745 0.909610 AGATCAACTCCAAGGGCCGA 60.910 55.000 0.00 0.00 0.00 5.54
693 746 0.745845 CAGATCAACTCCAAGGGCCG 60.746 60.000 0.00 0.00 0.00 6.13
694 747 0.394899 CCAGATCAACTCCAAGGGCC 60.395 60.000 0.00 0.00 0.00 5.80
698 753 2.082231 CACTGCCAGATCAACTCCAAG 58.918 52.381 0.00 0.00 0.00 3.61
708 763 1.267806 CGCTTTTTCACACTGCCAGAT 59.732 47.619 0.00 0.00 0.00 2.90
713 768 1.123655 GCTTCGCTTTTTCACACTGC 58.876 50.000 0.00 0.00 0.00 4.40
714 769 1.388888 CGCTTCGCTTTTTCACACTG 58.611 50.000 0.00 0.00 0.00 3.66
715 770 3.825812 CGCTTCGCTTTTTCACACT 57.174 47.368 0.00 0.00 0.00 3.55
732 787 2.811317 GAGGTCTGTGCTTCGGCG 60.811 66.667 0.00 0.00 45.37 6.46
733 788 2.435059 GGAGGTCTGTGCTTCGGC 60.435 66.667 0.00 0.00 42.19 5.54
734 789 2.125912 CGGAGGTCTGTGCTTCGG 60.126 66.667 0.00 0.00 0.00 4.30
735 790 2.811317 GCGGAGGTCTGTGCTTCG 60.811 66.667 0.00 0.00 0.00 3.79
736 791 2.811317 CGCGGAGGTCTGTGCTTC 60.811 66.667 0.00 0.00 0.00 3.86
737 792 3.616721 ACGCGGAGGTCTGTGCTT 61.617 61.111 12.47 0.00 36.24 3.91
738 793 4.363990 CACGCGGAGGTCTGTGCT 62.364 66.667 12.47 0.00 36.24 4.40
743 798 4.295119 AAACGCACGCGGAGGTCT 62.295 61.111 16.70 0.00 44.69 3.85
744 799 4.072088 CAAACGCACGCGGAGGTC 62.072 66.667 16.70 0.00 44.69 3.85
751 806 1.714899 ATATCCCAGCAAACGCACGC 61.715 55.000 0.00 0.00 0.00 5.34
918 1076 4.959596 GAGGATGGCGGCTCGAGC 62.960 72.222 29.38 29.38 41.14 5.03
919 1077 4.637489 CGAGGATGGCGGCTCGAG 62.637 72.222 11.43 8.45 41.24 4.04
1114 1839 2.211468 ATCAACTTTCCCGGGCCCTC 62.211 60.000 22.43 0.00 0.00 4.30
1133 1864 0.457853 GTACTCCGCGACTGCATGAA 60.458 55.000 8.23 0.00 42.97 2.57
1135 1866 1.878522 GGTACTCCGCGACTGCATG 60.879 63.158 8.23 0.00 42.97 4.06
1281 2121 2.031163 GCGACCAGGTGCTTGTCT 59.969 61.111 0.00 0.00 0.00 3.41
1403 2258 1.743252 GCTGTAGTCCTGCAGGTGC 60.743 63.158 31.58 23.97 42.45 5.01
1418 2279 1.379044 GACTGGAACCCCATGGCTG 60.379 63.158 6.09 1.56 42.59 4.85
1504 2374 1.071471 CGGCTTGGGAGTCTTGTGT 59.929 57.895 0.00 0.00 0.00 3.72
1838 2822 0.729140 GGGCTCGCGTTCAACAAATG 60.729 55.000 5.77 0.00 0.00 2.32
1933 2917 2.354704 CGTTAGCCCAGATGTCTCCAAA 60.355 50.000 0.00 0.00 0.00 3.28
1987 2971 1.975407 GGACAGGGAACGACGGAGA 60.975 63.158 0.00 0.00 0.00 3.71
2057 3041 2.037136 ACTAGTCGACGACCCACCG 61.037 63.158 23.76 10.50 32.18 4.94
2064 3054 1.661178 GCGTTGAACACTAGTCGACGA 60.661 52.381 21.04 3.61 32.49 4.20
2082 3072 3.186047 CGAAGCAAGTACCGGGCG 61.186 66.667 6.32 0.00 0.00 6.13
2087 3077 1.058404 GTCGACACGAAGCAAGTACC 58.942 55.000 11.55 0.00 37.72 3.34
2158 3151 2.330254 TTGCAAAGAGCTGGGAACG 58.670 52.632 0.00 0.00 45.94 3.95
2451 3468 5.305386 TCCCAGAATCATGAACGATGAGTAT 59.695 40.000 0.00 0.00 44.54 2.12
2894 4148 3.128068 TGTCATCATGATGTGCAAGAAGC 59.872 43.478 30.01 13.27 39.72 3.86
2973 4321 1.737793 GGGGTGAAGCTAATGACAACG 59.262 52.381 0.00 0.00 0.00 4.10
3029 4779 7.503566 ACGAACTACAAGTACCCTGCTATATTA 59.496 37.037 0.00 0.00 0.00 0.98
3205 4983 6.976925 CCAGGATGCTCTGAATTAAAATTGTC 59.023 38.462 0.00 0.00 36.93 3.18
3424 5203 2.352617 CGCTAGATTCCATCTCTCTGGC 60.353 54.545 0.00 0.00 40.76 4.85
3425 5204 3.153130 TCGCTAGATTCCATCTCTCTGG 58.847 50.000 0.00 0.00 40.76 3.86
3426 5205 3.820467 ACTCGCTAGATTCCATCTCTCTG 59.180 47.826 0.00 0.00 40.76 3.35
3678 5643 4.990257 AGGATTCATGCAAGAAAATGACG 58.010 39.130 8.64 0.00 32.63 4.35
3884 5850 9.410556 CACAGAACAAATATAACCAAGAAAAGG 57.589 33.333 0.00 0.00 0.00 3.11
3903 5869 0.682209 ATCCAGCCATGCCACAGAAC 60.682 55.000 0.00 0.00 0.00 3.01
4173 6139 4.162509 AGGGTTGCAGTATTTCTCTAGTCC 59.837 45.833 0.00 0.00 0.00 3.85
4183 6149 0.034089 GCCTCCAGGGTTGCAGTATT 60.034 55.000 0.00 0.00 37.43 1.89
4227 6193 1.772156 GAAGATAGGGGCAGGGGCT 60.772 63.158 0.00 0.00 40.87 5.19
4287 6253 2.584391 GGCAAGACTCACGACCCCT 61.584 63.158 0.00 0.00 0.00 4.79
4318 6284 0.805322 CTAGCTCCGCTGCAACTCTG 60.805 60.000 0.00 0.00 40.10 3.35
4347 6313 2.501128 GCCAGCACCTCTATCGCA 59.499 61.111 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.