Multiple sequence alignment - TraesCS2D01G477300

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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 TraesCS2D01G477300 chr2D 100.000 6125 0 0 1 6125 579384423 579390547 0.000000e+00 11311.0
1 TraesCS2D01G477300 chr2D 97.500 40 1 0 270 309 380407724 380407685 1.100000e-07 69.4
2 TraesCS2D01G477300 chr2A 95.369 4038 149 31 2117 6125 717137345 717141373 0.000000e+00 6386.0
3 TraesCS2D01G477300 chr2A 91.703 916 42 18 852 1765 717118756 717119639 0.000000e+00 1240.0
4 TraesCS2D01G477300 chr2A 85.649 871 50 29 1 854 717114888 717115700 0.000000e+00 846.0
5 TraesCS2D01G477300 chr2A 90.981 632 34 8 241 854 717113987 717114613 0.000000e+00 830.0
6 TraesCS2D01G477300 chr2A 84.151 795 58 20 77 854 717116091 717116834 0.000000e+00 708.0
7 TraesCS2D01G477300 chr2A 93.750 368 17 3 1756 2123 717119825 717120186 1.160000e-151 547.0
8 TraesCS2D01G477300 chr2A 87.260 416 31 6 77 491 717117226 717117620 7.240000e-124 455.0
9 TraesCS2D01G477300 chr2A 93.130 262 15 2 515 775 717117831 717118090 1.250000e-101 381.0
10 TraesCS2D01G477300 chr2A 93.151 219 9 5 589 805 717118534 717118748 3.560000e-82 316.0
11 TraesCS2D01G477300 chr2A 93.966 116 7 0 1 116 717115978 717116093 6.310000e-40 176.0
12 TraesCS2D01G477300 chr2A 92.241 116 9 0 1 116 717117113 717117228 1.370000e-36 165.0
13 TraesCS2D01G477300 chr2A 96.491 57 2 0 1 57 717113932 717113988 1.820000e-15 95.3
14 TraesCS2D01G477300 chr2B 93.934 3610 169 25 2551 6125 696670707 696674301 0.000000e+00 5408.0
15 TraesCS2D01G477300 chr2B 92.749 993 62 7 1548 2535 696669736 696670723 0.000000e+00 1426.0
16 TraesCS2D01G477300 chr2B 93.463 872 36 7 1 851 696666812 696667683 0.000000e+00 1275.0
17 TraesCS2D01G477300 chr2B 92.132 699 43 7 854 1544 696668217 696668911 0.000000e+00 976.0
18 TraesCS2D01G477300 chr2B 94.737 38 2 0 399 436 96585169 96585206 6.630000e-05 60.2
19 TraesCS2D01G477300 chr6A 80.380 2635 409 68 2559 5149 36108532 36105962 0.000000e+00 1903.0
20 TraesCS2D01G477300 chr6A 84.016 1001 139 16 2551 3550 36252435 36251455 0.000000e+00 942.0
21 TraesCS2D01G477300 chr6A 81.884 414 70 5 2124 2534 36252831 36252420 1.630000e-90 344.0
22 TraesCS2D01G477300 chr6B 79.841 2644 410 75 2559 5144 67130635 67128057 0.000000e+00 1816.0
23 TraesCS2D01G477300 chr6B 79.796 2643 413 77 2559 5144 67323157 67320579 0.000000e+00 1810.0
24 TraesCS2D01G477300 chr6B 79.077 2189 356 55 2559 4711 66970649 66968527 0.000000e+00 1411.0
25 TraesCS2D01G477300 chr6B 78.986 1618 273 45 3563 5145 66990425 66988840 0.000000e+00 1042.0
26 TraesCS2D01G477300 chr6B 84.263 1004 131 18 2551 3550 66991449 66990469 0.000000e+00 953.0
27 TraesCS2D01G477300 chr6B 84.474 979 129 20 2552 3529 68749332 68750288 0.000000e+00 944.0
28 TraesCS2D01G477300 chr6B 83.700 1000 139 21 2552 3550 68782816 68781840 0.000000e+00 922.0
29 TraesCS2D01G477300 chr6B 81.153 902 144 19 4247 5136 67409159 67408272 0.000000e+00 701.0
30 TraesCS2D01G477300 chr6B 77.329 1213 200 53 3563 4741 67228724 67227553 0.000000e+00 647.0
31 TraesCS2D01G477300 chr6B 84.748 636 82 10 2551 3183 67258337 67257714 1.870000e-174 623.0
32 TraesCS2D01G477300 chr6B 84.127 441 51 16 3569 3998 67409776 67409344 5.710000e-110 409.0
33 TraesCS2D01G477300 chr6B 80.769 442 73 9 2102 2535 67131064 67130627 9.840000e-88 335.0
34 TraesCS2D01G477300 chr6B 79.271 439 82 7 2103 2534 67258758 67258322 1.290000e-76 298.0
35 TraesCS2D01G477300 chr6B 83.521 267 40 2 2103 2365 68748921 68749187 4.740000e-61 246.0
36 TraesCS2D01G477300 chr6D 85.230 1002 124 17 2551 3550 31770128 31769149 0.000000e+00 1009.0
37 TraesCS2D01G477300 chr6D 85.141 996 122 20 2559 3550 31753995 31753022 0.000000e+00 996.0
38 TraesCS2D01G477300 chr6D 84.806 1007 123 21 2551 3550 23440011 23439028 0.000000e+00 985.0
39 TraesCS2D01G477300 chr6D 83.444 453 60 10 3563 4005 31769105 31768658 2.060000e-109 407.0
40 TraesCS2D01G477300 chr6D 82.328 481 69 11 3535 4005 23439011 23438537 2.660000e-108 403.0
41 TraesCS2D01G477300 chr6D 81.179 441 73 9 2102 2535 31754424 31753987 4.540000e-91 346.0
42 TraesCS2D01G477300 chr6D 79.727 439 77 8 2103 2534 23440429 23439996 2.140000e-79 307.0
43 TraesCS2D01G477300 chr6D 79.727 439 77 8 2103 2534 31770546 31770113 2.140000e-79 307.0
44 TraesCS2D01G477300 chr1D 80.672 119 19 4 4143 4259 154020752 154020636 8.460000e-14 89.8
45 TraesCS2D01G477300 chr1A 75.234 214 39 11 4048 4259 206794139 206794340 8.460000e-14 89.8
46 TraesCS2D01G477300 chr1B 79.231 130 24 3 4131 4259 223799626 223799499 3.040000e-13 87.9
47 TraesCS2D01G477300 chr5D 92.453 53 4 0 646 698 508618929 508618981 6.580000e-10 76.8
48 TraesCS2D01G477300 chr5D 100.000 28 0 0 277 304 95309585 95309558 1.100000e-02 52.8
49 TraesCS2D01G477300 chrUn 95.455 44 2 0 399 442 171672581 171672538 3.060000e-08 71.3
50 TraesCS2D01G477300 chrUn 97.561 41 1 0 399 439 171733749 171733789 3.060000e-08 71.3
51 TraesCS2D01G477300 chr7B 77.778 135 15 9 4110 4234 583483522 583483651 1.100000e-07 69.4
52 TraesCS2D01G477300 chr4A 80.682 88 14 3 4159 4245 596572274 596572189 1.430000e-06 65.8
53 TraesCS2D01G477300 chr5B 97.143 35 1 0 270 304 70795599 70795565 6.630000e-05 60.2
54 TraesCS2D01G477300 chr5A 88.889 45 5 0 399 443 380223976 380223932 8.580000e-04 56.5


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 TraesCS2D01G477300 chr2D 579384423 579390547 6124 False 11311.000000 11311 100.000000 1 6125 1 chr2D.!!$F1 6124
1 TraesCS2D01G477300 chr2A 717137345 717141373 4028 False 6386.000000 6386 95.369000 2117 6125 1 chr2A.!!$F1 4008
2 TraesCS2D01G477300 chr2A 717113932 717120186 6254 False 523.572727 1240 91.133909 1 2123 11 chr2A.!!$F2 2122
3 TraesCS2D01G477300 chr2B 696666812 696674301 7489 False 2271.250000 5408 93.069500 1 6125 4 chr2B.!!$F2 6124
4 TraesCS2D01G477300 chr6A 36105962 36108532 2570 True 1903.000000 1903 80.380000 2559 5149 1 chr6A.!!$R1 2590
5 TraesCS2D01G477300 chr6A 36251455 36252831 1376 True 643.000000 942 82.950000 2124 3550 2 chr6A.!!$R2 1426
6 TraesCS2D01G477300 chr6B 67320579 67323157 2578 True 1810.000000 1810 79.796000 2559 5144 1 chr6B.!!$R3 2585
7 TraesCS2D01G477300 chr6B 66968527 66970649 2122 True 1411.000000 1411 79.077000 2559 4711 1 chr6B.!!$R1 2152
8 TraesCS2D01G477300 chr6B 67128057 67131064 3007 True 1075.500000 1816 80.305000 2102 5144 2 chr6B.!!$R6 3042
9 TraesCS2D01G477300 chr6B 66988840 66991449 2609 True 997.500000 1042 81.624500 2551 5145 2 chr6B.!!$R5 2594
10 TraesCS2D01G477300 chr6B 68781840 68782816 976 True 922.000000 922 83.700000 2552 3550 1 chr6B.!!$R4 998
11 TraesCS2D01G477300 chr6B 67227553 67228724 1171 True 647.000000 647 77.329000 3563 4741 1 chr6B.!!$R2 1178
12 TraesCS2D01G477300 chr6B 68748921 68750288 1367 False 595.000000 944 83.997500 2103 3529 2 chr6B.!!$F1 1426
13 TraesCS2D01G477300 chr6B 67408272 67409776 1504 True 555.000000 701 82.640000 3569 5136 2 chr6B.!!$R8 1567
14 TraesCS2D01G477300 chr6B 67257714 67258758 1044 True 460.500000 623 82.009500 2103 3183 2 chr6B.!!$R7 1080
15 TraesCS2D01G477300 chr6D 31753022 31754424 1402 True 671.000000 996 83.160000 2102 3550 2 chr6D.!!$R2 1448
16 TraesCS2D01G477300 chr6D 31768658 31770546 1888 True 574.333333 1009 82.800333 2103 4005 3 chr6D.!!$R3 1902
17 TraesCS2D01G477300 chr6D 23438537 23440429 1892 True 565.000000 985 82.287000 2103 4005 3 chr6D.!!$R1 1902

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
925 5502 0.179037 TAAGGCATAGCAGCAGCAGG 60.179 55.000 3.17 0.00 45.49 4.85 F
1120 5719 1.202099 TTCACCGGTGGCCAGGAATA 61.202 55.000 33.40 8.84 0.00 1.75 F
1967 7590 0.689745 ACTATCGCCTGGCCAACCTA 60.690 55.000 14.12 0.00 36.63 3.08 F
2542 8188 0.263765 AGTACCTCCCTTATCCCGCA 59.736 55.000 0.00 0.00 0.00 5.69 F
2545 8191 0.996583 ACCTCCCTTATCCCGCAAAA 59.003 50.000 0.00 0.00 0.00 2.44 F
2546 8192 1.356398 ACCTCCCTTATCCCGCAAAAA 59.644 47.619 0.00 0.00 0.00 1.94 F
2716 8398 1.888512 GGGATGTTGAGCTTGCAAGAA 59.111 47.619 30.39 12.69 0.00 2.52 F
4526 10330 0.029681 ATCAGGCCCCTACACCAGAT 60.030 55.000 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 7571 0.689745 TAGGTTGGCCAGGCGATAGT 60.690 55.000 5.11 0.0 37.19 2.12 R
2526 8172 0.996583 TTTTGCGGGATAAGGGAGGT 59.003 50.000 0.00 0.0 0.00 3.85 R
3805 9564 0.879765 AGTGAATCAACAGCAGCAGC 59.120 50.000 0.00 0.0 42.56 5.25 R
3806 9565 1.467734 GGAGTGAATCAACAGCAGCAG 59.532 52.381 0.00 0.0 0.00 4.24 R
3807 9566 1.527034 GGAGTGAATCAACAGCAGCA 58.473 50.000 0.00 0.0 0.00 4.41 R
4100 9867 2.288643 GGGAGGGAGAGGGCAGAT 59.711 66.667 0.00 0.0 0.00 2.90 R
4650 10454 1.390565 AGCCTCATGATCTTTGCAGC 58.609 50.000 0.00 0.0 0.00 5.25 R
5801 11637 0.108138 GTCTGCGACAGGCTTATGGT 60.108 55.000 4.51 0.0 44.05 3.55 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
40 41 5.310857 ACCAAATTCTCTCCAAGAGGTAGTT 59.689 40.000 4.24 0.00 42.54 2.24
182 1138 1.768112 AAAGCGTACGTGTGCACCAC 61.768 55.000 17.90 11.53 40.89 4.16
248 1204 8.882736 TCTTGTTCATCACAATCATACATACAC 58.117 33.333 0.00 0.00 44.72 2.90
250 1206 8.558973 TGTTCATCACAATCATACATACACAA 57.441 30.769 0.00 0.00 29.87 3.33
254 1210 9.176460 TCATCACAATCATACATACACAAATGT 57.824 29.630 0.00 0.00 42.62 2.71
293 1249 5.704515 GTGCTAGATACATCCATTTGAGCAT 59.295 40.000 0.00 0.00 39.39 3.79
374 1331 5.564550 ACATGCTGAGGAAACTGAGTAAAT 58.435 37.500 0.00 0.00 44.41 1.40
485 1442 8.897872 TTAATGGACTCGTTCCCTATATTTTC 57.102 34.615 3.76 0.00 45.17 2.29
762 4173 5.734786 GCTGGGGTTTATTTTTGTTTTTGGC 60.735 40.000 0.00 0.00 0.00 4.52
763 4174 4.335594 TGGGGTTTATTTTTGTTTTTGGCG 59.664 37.500 0.00 0.00 0.00 5.69
768 4179 7.219154 GGGTTTATTTTTGTTTTTGGCGAAAAG 59.781 33.333 12.86 0.00 37.88 2.27
775 4814 3.365220 TGTTTTTGGCGAAAAGAACAACG 59.635 39.130 12.86 0.00 37.88 4.10
778 4817 0.302288 TGGCGAAAAGAACAACGACG 59.698 50.000 0.00 0.00 36.51 5.12
781 4820 1.902749 CGAAAAGAACAACGACGACG 58.097 50.000 5.58 5.58 45.75 5.12
797 4836 1.202211 CGACGACGATGGATGGTACAA 60.202 52.381 0.00 0.00 42.31 2.41
851 4890 0.307146 GGATCGATGCAGCTTCAAGC 59.693 55.000 12.54 0.00 42.84 4.01
853 4892 1.099879 ATCGATGCAGCTTCAAGCCC 61.100 55.000 5.53 0.00 43.77 5.19
917 5494 1.419381 TCCGTCCATAAGGCATAGCA 58.581 50.000 0.00 0.00 33.74 3.49
920 5497 1.541015 CGTCCATAAGGCATAGCAGCA 60.541 52.381 0.00 0.00 35.83 4.41
923 5500 1.601166 CATAAGGCATAGCAGCAGCA 58.399 50.000 3.17 0.00 45.49 4.41
924 5501 1.535896 CATAAGGCATAGCAGCAGCAG 59.464 52.381 3.17 0.00 45.49 4.24
925 5502 0.179037 TAAGGCATAGCAGCAGCAGG 60.179 55.000 3.17 0.00 45.49 4.85
926 5503 2.124403 GGCATAGCAGCAGCAGGT 60.124 61.111 3.17 0.00 45.49 4.00
952 5529 3.518303 TGCTCATCTCATATCATCCAGGG 59.482 47.826 0.00 0.00 0.00 4.45
963 5562 8.418597 TCATATCATCCAGGGTAGTAAGTTAC 57.581 38.462 4.78 4.78 0.00 2.50
964 5563 7.453752 TCATATCATCCAGGGTAGTAAGTTACC 59.546 40.741 9.46 0.00 41.98 2.85
965 5564 5.216665 TCATCCAGGGTAGTAAGTTACCT 57.783 43.478 9.46 0.00 42.28 3.08
966 5565 6.345646 TCATCCAGGGTAGTAAGTTACCTA 57.654 41.667 9.46 0.00 42.28 3.08
967 5566 6.744822 TCATCCAGGGTAGTAAGTTACCTAA 58.255 40.000 9.46 0.00 42.28 2.69
968 5567 7.367828 TCATCCAGGGTAGTAAGTTACCTAAT 58.632 38.462 9.46 0.00 42.28 1.73
969 5568 7.847848 TCATCCAGGGTAGTAAGTTACCTAATT 59.152 37.037 9.46 0.00 42.28 1.40
970 5569 9.151177 CATCCAGGGTAGTAAGTTACCTAATTA 57.849 37.037 9.46 0.00 42.28 1.40
971 5570 8.773033 TCCAGGGTAGTAAGTTACCTAATTAG 57.227 38.462 9.46 5.43 42.28 1.73
972 5571 7.288621 TCCAGGGTAGTAAGTTACCTAATTAGC 59.711 40.741 9.46 4.95 42.28 3.09
973 5572 7.440198 CAGGGTAGTAAGTTACCTAATTAGCC 58.560 42.308 14.90 14.90 42.28 3.93
974 5573 7.289549 CAGGGTAGTAAGTTACCTAATTAGCCT 59.710 40.741 17.73 17.73 42.28 4.58
975 5574 8.514504 AGGGTAGTAAGTTACCTAATTAGCCTA 58.485 37.037 20.23 0.00 42.28 3.93
976 5575 8.580720 GGGTAGTAAGTTACCTAATTAGCCTAC 58.419 40.741 9.46 4.35 42.28 3.18
977 5576 9.360901 GGTAGTAAGTTACCTAATTAGCCTACT 57.639 37.037 9.46 6.41 40.00 2.57
983 5582 8.835550 AGTTACCTAATTAGCCTACTTAGTGT 57.164 34.615 6.99 7.65 0.00 3.55
984 5583 9.927081 AGTTACCTAATTAGCCTACTTAGTGTA 57.073 33.333 6.99 6.94 0.00 2.90
1001 5600 5.836821 AGTGTATCATCTGTACGTGACAT 57.163 39.130 0.00 0.00 37.45 3.06
1033 5632 2.802816 GCTAGCCGACTACCATTCATTG 59.197 50.000 2.29 0.00 0.00 2.82
1120 5719 1.202099 TTCACCGGTGGCCAGGAATA 61.202 55.000 33.40 8.84 0.00 1.75
1123 5722 1.205460 ACCGGTGGCCAGGAATACTT 61.205 55.000 17.65 0.00 0.00 2.24
1325 5926 2.030185 ACGTGAGATACAGTCGTTTGCT 60.030 45.455 0.00 0.00 29.25 3.91
1567 6995 9.311916 GATTAAAATTAGCATGCATGTTTACCA 57.688 29.630 26.79 10.13 0.00 3.25
1586 7014 4.383173 ACCACCGTTTTCTAGTTACCTTG 58.617 43.478 0.00 0.00 0.00 3.61
1710 7138 4.592942 ACCTCAAGCTAGCAATTCATGAA 58.407 39.130 18.83 11.26 0.00 2.57
1769 7392 2.917600 TCCTAGAGTGACACCTACTCCA 59.082 50.000 0.84 0.00 44.35 3.86
1786 7409 5.495926 ACTCCAGAACTGATGAGAAACAT 57.504 39.130 12.49 0.00 42.47 2.71
1967 7590 0.689745 ACTATCGCCTGGCCAACCTA 60.690 55.000 14.12 0.00 36.63 3.08
2381 8019 8.235226 GGTAAGTAAAGGAAAATCTTAGTGTGC 58.765 37.037 0.00 0.00 0.00 4.57
2518 8164 2.143122 CTAGCGTTTTCTTGTGGAGCA 58.857 47.619 0.00 0.00 0.00 4.26
2519 8165 1.609208 AGCGTTTTCTTGTGGAGCAT 58.391 45.000 0.00 0.00 0.00 3.79
2520 8166 2.778299 AGCGTTTTCTTGTGGAGCATA 58.222 42.857 0.00 0.00 0.00 3.14
2521 8167 3.347216 AGCGTTTTCTTGTGGAGCATAT 58.653 40.909 0.00 0.00 0.00 1.78
2522 8168 4.513442 AGCGTTTTCTTGTGGAGCATATA 58.487 39.130 0.00 0.00 0.00 0.86
2523 8169 4.941263 AGCGTTTTCTTGTGGAGCATATAA 59.059 37.500 0.00 0.00 0.00 0.98
2524 8170 5.065218 AGCGTTTTCTTGTGGAGCATATAAG 59.935 40.000 0.00 0.00 0.00 1.73
2525 8171 5.163754 GCGTTTTCTTGTGGAGCATATAAGT 60.164 40.000 0.00 0.00 0.00 2.24
2526 8172 6.036735 GCGTTTTCTTGTGGAGCATATAAGTA 59.963 38.462 0.00 0.00 0.00 2.24
2527 8173 7.399523 CGTTTTCTTGTGGAGCATATAAGTAC 58.600 38.462 0.00 0.00 0.00 2.73
2528 8174 7.465513 CGTTTTCTTGTGGAGCATATAAGTACC 60.466 40.741 0.00 0.00 0.00 3.34
2529 8175 6.808321 TTCTTGTGGAGCATATAAGTACCT 57.192 37.500 0.00 0.00 0.00 3.08
2530 8176 6.406692 TCTTGTGGAGCATATAAGTACCTC 57.593 41.667 0.00 0.00 0.00 3.85
2531 8177 5.304614 TCTTGTGGAGCATATAAGTACCTCC 59.695 44.000 5.42 5.42 41.87 4.30
2532 8178 3.901844 TGTGGAGCATATAAGTACCTCCC 59.098 47.826 8.92 3.08 41.03 4.30
2533 8179 4.161102 GTGGAGCATATAAGTACCTCCCT 58.839 47.826 8.92 0.00 41.03 4.20
2534 8180 4.593634 GTGGAGCATATAAGTACCTCCCTT 59.406 45.833 8.92 0.00 41.03 3.95
2535 8181 5.778750 GTGGAGCATATAAGTACCTCCCTTA 59.221 44.000 8.92 0.00 41.03 2.69
2536 8182 6.440965 GTGGAGCATATAAGTACCTCCCTTAT 59.559 42.308 8.92 0.00 41.03 1.73
2537 8183 6.668283 TGGAGCATATAAGTACCTCCCTTATC 59.332 42.308 8.92 0.00 41.03 1.75
2538 8184 6.098552 GGAGCATATAAGTACCTCCCTTATCC 59.901 46.154 1.73 0.00 36.68 2.59
2539 8185 5.965091 AGCATATAAGTACCTCCCTTATCCC 59.035 44.000 0.00 0.00 36.68 3.85
2540 8186 5.163437 GCATATAAGTACCTCCCTTATCCCG 60.163 48.000 0.00 0.00 36.68 5.14
2541 8187 1.421480 AAGTACCTCCCTTATCCCGC 58.579 55.000 0.00 0.00 0.00 6.13
2542 8188 0.263765 AGTACCTCCCTTATCCCGCA 59.736 55.000 0.00 0.00 0.00 5.69
2543 8189 1.125633 GTACCTCCCTTATCCCGCAA 58.874 55.000 0.00 0.00 0.00 4.85
2544 8190 1.487558 GTACCTCCCTTATCCCGCAAA 59.512 52.381 0.00 0.00 0.00 3.68
2545 8191 0.996583 ACCTCCCTTATCCCGCAAAA 59.003 50.000 0.00 0.00 0.00 2.44
2546 8192 1.356398 ACCTCCCTTATCCCGCAAAAA 59.644 47.619 0.00 0.00 0.00 1.94
2638 8320 3.693085 ACAACATGGCAGATGATGTTCTC 59.307 43.478 0.00 0.00 40.12 2.87
2682 8364 2.762327 GTGATTTCAACCATGGGCTCAT 59.238 45.455 18.09 0.00 0.00 2.90
2716 8398 1.888512 GGGATGTTGAGCTTGCAAGAA 59.111 47.619 30.39 12.69 0.00 2.52
2911 8593 2.038557 GAGTTACCTCCAGAACTTGCCA 59.961 50.000 0.00 0.00 36.04 4.92
3233 8926 5.474876 GTGGATGGATTTAGGATTGGCTAAG 59.525 44.000 0.00 0.00 0.00 2.18
3550 9257 5.065218 CCAACCGGATATTCAGACTTCTTTG 59.935 44.000 9.46 0.00 0.00 2.77
4100 9867 9.074443 GTTTTTGTGTTACGTTCCTTTATTTCA 57.926 29.630 0.00 0.00 0.00 2.69
4273 10050 3.906720 TCAATTAGCGGCTAAAGTCCT 57.093 42.857 24.71 6.75 29.35 3.85
4332 10112 4.668576 AGTAAGTCACATTGATTGCACG 57.331 40.909 0.00 0.00 0.00 5.34
4521 10309 7.364497 GGTTATATACTAATCAGGCCCCTACAC 60.364 44.444 0.00 0.00 0.00 2.90
4526 10330 0.029681 ATCAGGCCCCTACACCAGAT 60.030 55.000 0.00 0.00 0.00 2.90
4650 10454 0.943359 GCTTCGGATCATCTCCTGCG 60.943 60.000 0.00 0.00 42.47 5.18
4680 10484 1.026718 CATGAGGCTTTGGGACGACC 61.027 60.000 0.00 0.00 40.81 4.79
4711 10515 4.890581 TGCAAAGGTTATAACACACCAACT 59.109 37.500 17.16 0.65 35.25 3.16
4712 10516 5.219633 GCAAAGGTTATAACACACCAACTG 58.780 41.667 17.16 4.25 35.25 3.16
4715 10522 7.468906 GCAAAGGTTATAACACACCAACTGTAA 60.469 37.037 17.16 0.00 35.25 2.41
4722 10529 5.744666 AACACACCAACTGTAACACATAC 57.255 39.130 0.00 0.00 34.92 2.39
4742 10549 2.695666 ACGACTGCAGGATTAGCACTAT 59.304 45.455 19.93 0.00 37.02 2.12
4746 10553 4.446371 ACTGCAGGATTAGCACTATCAAC 58.554 43.478 19.93 0.00 37.02 3.18
4950 10785 1.953138 CGTGCTGGAGATGATCGCC 60.953 63.158 8.37 8.37 36.83 5.54
4977 10812 2.333069 TGGCAGGATCTGAATAGGGAG 58.667 52.381 0.00 0.00 32.44 4.30
5013 10848 5.234752 ACAAAGTCAACACTATCGCATACA 58.765 37.500 0.00 0.00 30.14 2.29
5199 11034 1.767654 GCAATGGGGTTTTGTGGCCT 61.768 55.000 3.32 0.00 0.00 5.19
5261 11097 5.769662 TCAAACATGAACTGAACAGCCTAAT 59.230 36.000 0.00 0.00 0.00 1.73
5268 11104 4.307032 ACTGAACAGCCTAATTGTGGAT 57.693 40.909 1.46 0.00 0.00 3.41
5282 11118 7.233757 CCTAATTGTGGATCTAGGCTACTAACT 59.766 40.741 0.00 0.00 0.00 2.24
5349 11185 5.335976 CGCTACTGGATCTATGATAGTTGCA 60.336 44.000 13.11 4.94 39.11 4.08
5371 11207 5.698545 GCATCGAGTGGCTTATAGAATCTTT 59.301 40.000 0.00 0.00 0.00 2.52
5492 11328 2.855209 ATGCAGCTTCAGAGTGAACT 57.145 45.000 0.00 0.00 32.21 3.01
5521 11357 3.716195 CATGGCCAGGACGTCCCA 61.716 66.667 30.82 21.17 37.41 4.37
5622 11458 2.909292 TAGGCCCTCCCCAAGGTAGC 62.909 65.000 0.00 0.00 44.56 3.58
5653 11489 5.676079 GCTCTGAAGACATCTGACTACTGAC 60.676 48.000 0.00 0.00 33.08 3.51
5696 11532 7.012989 TCCAATGAATCTTTATCATCTGCACTG 59.987 37.037 0.00 0.00 36.53 3.66
5699 11535 5.526479 TGAATCTTTATCATCTGCACTGCTC 59.474 40.000 1.98 0.00 0.00 4.26
5711 11547 1.522806 ACTGCTCGAAACAACGGCA 60.523 52.632 0.00 0.00 37.65 5.69
5732 11568 1.506493 CACTCGGCTGATTCATAGGC 58.494 55.000 0.00 0.00 37.37 3.93
5741 11577 4.991687 GGCTGATTCATAGGCTTGTAGTAC 59.008 45.833 0.00 0.00 37.70 2.73
5746 11582 5.593679 TTCATAGGCTTGTAGTACTCACC 57.406 43.478 0.00 0.27 0.00 4.02
5747 11583 4.606210 TCATAGGCTTGTAGTACTCACCA 58.394 43.478 0.00 0.00 0.00 4.17
5750 11586 4.004196 AGGCTTGTAGTACTCACCAAAC 57.996 45.455 0.00 0.00 0.00 2.93
5804 11640 4.383861 CTCGCTGAGCCTGCACCA 62.384 66.667 0.00 0.00 0.00 4.17
5870 11706 6.500336 TCTAGGGTCTAGAACAACAGGTATT 58.500 40.000 10.60 0.00 0.00 1.89
6090 11927 5.775686 TCAAAATCTTGCAAATGGACTCAG 58.224 37.500 0.00 0.00 32.14 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 1204 6.071221 AGCACCCCAATATGCATATACATTTG 60.071 38.462 19.39 13.62 44.59 2.32
250 1206 5.582953 AGCACCCCAATATGCATATACATT 58.417 37.500 19.39 3.06 44.59 2.71
254 1210 6.829985 ATCTAGCACCCCAATATGCATATA 57.170 37.500 19.39 0.00 44.59 0.86
265 1221 2.487746 TGGATGTATCTAGCACCCCA 57.512 50.000 0.00 0.00 0.00 4.96
293 1249 2.442413 CCTTTGCCCCGAATTACTTGA 58.558 47.619 0.00 0.00 0.00 3.02
374 1331 9.211485 GTAGTTACTAGCAACAAGTCCATTAAA 57.789 33.333 8.54 0.00 0.00 1.52
730 4140 2.386829 ATAAACCCCAGCCATCATGG 57.613 50.000 0.00 0.00 41.55 3.66
762 4173 1.513994 TCGTCGTCGTTGTTCTTTTCG 59.486 47.619 1.33 0.00 38.33 3.46
763 4174 2.652181 CGTCGTCGTCGTTGTTCTTTTC 60.652 50.000 3.67 0.00 38.33 2.29
768 4179 0.357894 CATCGTCGTCGTCGTTGTTC 59.642 55.000 11.41 0.00 38.33 3.18
775 4814 0.659427 TACCATCCATCGTCGTCGTC 59.341 55.000 1.33 0.00 38.33 4.20
778 4817 2.572191 TTGTACCATCCATCGTCGTC 57.428 50.000 0.00 0.00 0.00 4.20
781 4820 2.104111 TGGGATTGTACCATCCATCGTC 59.896 50.000 23.53 9.48 38.68 4.20
797 4836 4.012374 GTGACTGATGTGTGAATTGGGAT 58.988 43.478 0.00 0.00 0.00 3.85
851 4890 2.576648 GCCTCCAGGTTTATATAGGGGG 59.423 54.545 0.30 0.30 43.16 5.40
853 4892 4.848357 CATGCCTCCAGGTTTATATAGGG 58.152 47.826 0.00 0.00 37.57 3.53
923 5500 6.127111 GGATGATATGAGATGAGCATGTACCT 60.127 42.308 0.00 0.00 0.00 3.08
924 5501 6.047870 GGATGATATGAGATGAGCATGTACC 58.952 44.000 0.00 0.00 0.00 3.34
925 5502 6.637657 TGGATGATATGAGATGAGCATGTAC 58.362 40.000 0.00 0.00 0.00 2.90
926 5503 6.127140 CCTGGATGATATGAGATGAGCATGTA 60.127 42.308 0.00 0.00 0.00 2.29
966 5565 9.148879 ACAGATGATACACTAAGTAGGCTAATT 57.851 33.333 12.27 12.27 35.85 1.40
967 5566 8.713708 ACAGATGATACACTAAGTAGGCTAAT 57.286 34.615 0.00 0.00 35.85 1.73
968 5567 9.064706 GTACAGATGATACACTAAGTAGGCTAA 57.935 37.037 0.00 0.00 35.85 3.09
969 5568 7.387122 CGTACAGATGATACACTAAGTAGGCTA 59.613 40.741 0.00 0.00 35.85 3.93
970 5569 6.205076 CGTACAGATGATACACTAAGTAGGCT 59.795 42.308 0.00 0.00 35.85 4.58
971 5570 6.017275 ACGTACAGATGATACACTAAGTAGGC 60.017 42.308 0.00 0.00 35.85 3.93
972 5571 7.226128 TCACGTACAGATGATACACTAAGTAGG 59.774 40.741 0.00 0.00 35.85 3.18
973 5572 8.063038 GTCACGTACAGATGATACACTAAGTAG 58.937 40.741 0.00 0.00 35.85 2.57
974 5573 7.550196 TGTCACGTACAGATGATACACTAAGTA 59.450 37.037 0.00 0.00 33.49 2.24
975 5574 6.373495 TGTCACGTACAGATGATACACTAAGT 59.627 38.462 0.00 0.00 33.01 2.24
976 5575 6.782150 TGTCACGTACAGATGATACACTAAG 58.218 40.000 0.00 0.00 33.01 2.18
977 5576 6.746745 TGTCACGTACAGATGATACACTAA 57.253 37.500 0.00 0.00 33.01 2.24
978 5577 6.725246 CATGTCACGTACAGATGATACACTA 58.275 40.000 0.00 0.00 42.70 2.74
979 5578 5.582550 CATGTCACGTACAGATGATACACT 58.417 41.667 0.00 0.00 42.70 3.55
980 5579 4.207224 GCATGTCACGTACAGATGATACAC 59.793 45.833 7.73 0.00 42.70 2.90
981 5580 4.359706 GCATGTCACGTACAGATGATACA 58.640 43.478 7.73 0.00 42.70 2.29
982 5581 3.736252 GGCATGTCACGTACAGATGATAC 59.264 47.826 7.73 0.00 42.70 2.24
983 5582 3.383185 TGGCATGTCACGTACAGATGATA 59.617 43.478 0.00 0.00 42.70 2.15
984 5583 2.168313 TGGCATGTCACGTACAGATGAT 59.832 45.455 0.00 0.00 42.70 2.45
1001 5600 1.218047 CGGCTAGCTAAGTGTGGCA 59.782 57.895 15.72 0.00 32.62 4.92
1033 5632 0.450983 GCAGCAGCCATCAGTTTCTC 59.549 55.000 0.00 0.00 33.58 2.87
1114 5713 0.541863 CTGGTCCGGCAAGTATTCCT 59.458 55.000 0.00 0.00 0.00 3.36
1120 5719 4.681978 GCGACTGGTCCGGCAAGT 62.682 66.667 5.70 5.70 33.05 3.16
1123 5722 4.980805 GTTGCGACTGGTCCGGCA 62.981 66.667 0.00 0.00 0.00 5.69
1508 6114 7.156673 AGGTTGAATTTTGACCATGATTTGAG 58.843 34.615 0.00 0.00 35.89 3.02
1586 7014 4.799917 GCACTATCTTCGAAATCTACCCCC 60.800 50.000 0.00 0.00 0.00 5.40
1769 7392 8.099537 ACACATCTTATGTTTCTCATCAGTTCT 58.900 33.333 0.00 0.00 42.70 3.01
1948 7571 0.689745 TAGGTTGGCCAGGCGATAGT 60.690 55.000 5.11 0.00 37.19 2.12
2095 7718 9.435688 ACACAAAGAGCAAACTTCTTTATTTTT 57.564 25.926 0.43 0.00 33.05 1.94
2096 7719 8.872845 CACACAAAGAGCAAACTTCTTTATTTT 58.127 29.630 0.43 0.00 33.05 1.82
2097 7720 8.250332 TCACACAAAGAGCAAACTTCTTTATTT 58.750 29.630 0.43 0.00 33.05 1.40
2098 7721 7.702348 GTCACACAAAGAGCAAACTTCTTTATT 59.298 33.333 0.43 0.00 33.05 1.40
2099 7722 7.148086 TGTCACACAAAGAGCAAACTTCTTTAT 60.148 33.333 0.43 0.00 33.05 1.40
2381 8019 9.357652 CCAAATTCTTGTGTTTATCTTACATGG 57.642 33.333 0.00 0.00 0.00 3.66
2480 8124 8.547967 AACGCTAGAATTTATTTGAGACTTCA 57.452 30.769 0.00 0.00 0.00 3.02
2488 8132 8.638565 CCACAAGAAAACGCTAGAATTTATTTG 58.361 33.333 0.00 4.44 0.00 2.32
2518 8164 4.961099 GCGGGATAAGGGAGGTACTTATAT 59.039 45.833 0.00 0.00 41.55 0.86
2519 8165 4.202706 TGCGGGATAAGGGAGGTACTTATA 60.203 45.833 0.00 0.00 41.55 0.98
2520 8166 3.171528 GCGGGATAAGGGAGGTACTTAT 58.828 50.000 0.00 0.00 41.55 1.73
2521 8167 2.091166 TGCGGGATAAGGGAGGTACTTA 60.091 50.000 0.00 0.00 41.55 2.24
2522 8168 1.343681 TGCGGGATAAGGGAGGTACTT 60.344 52.381 0.00 0.00 41.55 2.24
2524 8170 1.125633 TTGCGGGATAAGGGAGGTAC 58.874 55.000 0.00 0.00 0.00 3.34
2525 8171 1.882308 TTTGCGGGATAAGGGAGGTA 58.118 50.000 0.00 0.00 0.00 3.08
2526 8172 0.996583 TTTTGCGGGATAAGGGAGGT 59.003 50.000 0.00 0.00 0.00 3.85
2527 8173 2.137810 TTTTTGCGGGATAAGGGAGG 57.862 50.000 0.00 0.00 0.00 4.30
2545 8191 7.837689 GTCCCAAGGGAGGTAATTATACTTTTT 59.162 37.037 8.41 0.00 46.16 1.94
2546 8192 7.351952 GTCCCAAGGGAGGTAATTATACTTTT 58.648 38.462 8.41 0.00 46.16 2.27
2547 8193 6.408891 CGTCCCAAGGGAGGTAATTATACTTT 60.409 42.308 17.60 0.00 46.16 2.66
2548 8194 5.071384 CGTCCCAAGGGAGGTAATTATACTT 59.929 44.000 17.60 0.00 46.16 2.24
2549 8195 4.591924 CGTCCCAAGGGAGGTAATTATACT 59.408 45.833 17.60 0.00 46.16 2.12
2638 8320 5.125417 ACCATTATCATTTGTGAACTTCCGG 59.875 40.000 0.00 0.00 0.00 5.14
2682 8364 6.373005 TCAACATCCCTCTAATGTCTTTGA 57.627 37.500 0.00 0.00 36.35 2.69
2716 8398 4.474651 TCTCCCATGTTGAGGTATGACATT 59.525 41.667 9.01 0.00 32.01 2.71
2911 8593 8.105829 AGATTCTCAATTGATGTGTTCCTAGTT 58.894 33.333 8.96 0.00 0.00 2.24
3014 8696 9.838339 CATGGAAGGAGAGTAGTTTATTATGTT 57.162 33.333 0.00 0.00 0.00 2.71
3233 8926 1.384222 CCCTTGCAGCCGGTATTTCC 61.384 60.000 1.90 0.00 0.00 3.13
3754 9507 9.950496 AATCTGTGTGTGAAACTTCTATAAGAT 57.050 29.630 0.00 0.00 38.04 2.40
3805 9564 0.879765 AGTGAATCAACAGCAGCAGC 59.120 50.000 0.00 0.00 42.56 5.25
3806 9565 1.467734 GGAGTGAATCAACAGCAGCAG 59.532 52.381 0.00 0.00 0.00 4.24
3807 9566 1.527034 GGAGTGAATCAACAGCAGCA 58.473 50.000 0.00 0.00 0.00 4.41
3968 9727 9.500701 TTTAGCTCCTTGGGGAAATTAAATTAT 57.499 29.630 0.00 0.00 41.69 1.28
4100 9867 2.288643 GGGAGGGAGAGGGCAGAT 59.711 66.667 0.00 0.00 0.00 2.90
4186 9953 2.660189 GCAAATAAGGCATGTGCAGT 57.340 45.000 7.36 0.00 45.90 4.40
4332 10112 2.979814 ACAGGGCACAAAAACTTTCC 57.020 45.000 0.00 0.00 0.00 3.13
4420 10204 9.408648 GTAAAATGAAGGAAGGGAAGATGAATA 57.591 33.333 0.00 0.00 0.00 1.75
4430 10214 7.119846 CACTGTAAGAGTAAAATGAAGGAAGGG 59.880 40.741 0.00 0.00 37.43 3.95
4521 10309 6.240549 ACCATTTCTTAGGTAGTCATCTGG 57.759 41.667 0.00 0.00 36.07 3.86
4526 10330 6.604396 TGACGATACCATTTCTTAGGTAGTCA 59.396 38.462 8.67 8.67 43.15 3.41
4650 10454 1.390565 AGCCTCATGATCTTTGCAGC 58.609 50.000 0.00 0.00 0.00 5.25
4680 10484 1.549203 ATAACCTTTGCACTGCCCAG 58.451 50.000 0.00 0.00 0.00 4.45
4711 10515 2.559231 TCCTGCAGTCGTATGTGTTACA 59.441 45.455 13.81 0.00 0.00 2.41
4712 10516 3.226346 TCCTGCAGTCGTATGTGTTAC 57.774 47.619 13.81 0.00 0.00 2.50
4715 10522 3.738281 GCTAATCCTGCAGTCGTATGTGT 60.738 47.826 13.81 0.00 0.00 3.72
4722 10529 2.871182 TAGTGCTAATCCTGCAGTCG 57.129 50.000 13.81 0.00 42.36 4.18
4784 10618 3.573110 TCAATGTTGATGTGGATGCACAA 59.427 39.130 24.45 7.67 38.69 3.33
4933 10768 1.953138 CGGCGATCATCTCCAGCAC 60.953 63.158 0.00 0.00 0.00 4.40
4950 10785 0.178767 TCAGATCCTGCCATTCACCG 59.821 55.000 0.00 0.00 0.00 4.94
4977 10812 2.147150 GACTTTGTCCCAGAGAAGCAC 58.853 52.381 0.00 0.00 0.00 4.40
5013 10848 1.144057 GAGTGACGCCCCGATGAAT 59.856 57.895 0.00 0.00 0.00 2.57
5173 11008 0.681175 AAAACCCCATTGCAGAGCAC 59.319 50.000 0.00 0.00 38.71 4.40
5177 11012 1.047002 CCACAAAACCCCATTGCAGA 58.953 50.000 0.00 0.00 0.00 4.26
5178 11013 0.603439 GCCACAAAACCCCATTGCAG 60.603 55.000 0.00 0.00 0.00 4.41
5227 11062 8.345565 GTTCAGTTCATGTTTGACTAGATGTTT 58.654 33.333 0.00 0.00 0.00 2.83
5261 11097 5.955959 TGAAGTTAGTAGCCTAGATCCACAA 59.044 40.000 0.00 0.00 0.00 3.33
5268 11104 6.436218 TGTTCATGTGAAGTTAGTAGCCTAGA 59.564 38.462 0.00 0.00 34.27 2.43
5282 11118 5.904941 AGAACTTTTGCATGTTCATGTGAA 58.095 33.333 21.48 6.73 43.38 3.18
5349 11185 5.698545 GCAAAGATTCTATAAGCCACTCGAT 59.301 40.000 0.00 0.00 0.00 3.59
5371 11207 4.800023 AGATTGGATGAGATGAAATGGCA 58.200 39.130 0.00 0.00 0.00 4.92
5471 11307 3.252701 CAGTTCACTCTGAAGCTGCATTT 59.747 43.478 0.00 0.00 37.00 2.32
5477 11313 1.690893 TCTGCAGTTCACTCTGAAGCT 59.309 47.619 14.67 0.00 40.06 3.74
5521 11357 3.864686 CGCTTGCGGCTATTGCGT 61.865 61.111 7.16 0.00 41.45 5.24
5622 11458 3.872182 CAGATGTCTTCAGAGCTTGATGG 59.128 47.826 0.00 0.00 35.27 3.51
5653 11489 2.940158 TGGAAGATTGGGATGAGCATG 58.060 47.619 0.00 0.00 0.00 4.06
5696 11532 2.251371 GGTGCCGTTGTTTCGAGC 59.749 61.111 0.00 0.00 0.00 5.03
5699 11535 1.278637 GAGTGGTGCCGTTGTTTCG 59.721 57.895 0.00 0.00 0.00 3.46
5711 11547 1.414181 CCTATGAATCAGCCGAGTGGT 59.586 52.381 0.00 0.00 37.67 4.16
5732 11568 5.465724 GGAACTGTTTGGTGAGTACTACAAG 59.534 44.000 0.00 0.00 0.00 3.16
5801 11637 0.108138 GTCTGCGACAGGCTTATGGT 60.108 55.000 4.51 0.00 44.05 3.55
5804 11640 1.141881 CCGTCTGCGACAGGCTTAT 59.858 57.895 9.24 0.00 44.05 1.73
5870 11706 3.069016 AGAACTCATACGTGTGGTTGTCA 59.931 43.478 18.63 0.00 0.00 3.58
6090 11927 5.598830 TGTCTCCAGAAGATATGGGAGTTAC 59.401 44.000 6.45 0.02 45.65 2.50


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

AutoCloner maintained by Alex Coulton.