Multiple sequence alignment - TraesCS4A01G492600

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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 TraesCS4A01G492600 chr4A 100.000 5623 0 0 1 5623 741544979 741550601 0.000000e+00 10384.0
1 TraesCS4A01G492600 chr4A 94.219 986 57 0 1 986 69894491 69895476 0.000000e+00 1506.0
2 TraesCS4A01G492600 chr4A 83.162 291 49 0 3345 3635 88519153 88518863 3.340000e-67 267.0
3 TraesCS4A01G492600 chr6D 91.776 1897 134 16 1016 2905 471918859 471920740 0.000000e+00 2619.0
4 TraesCS4A01G492600 chr6D 90.901 1121 71 15 3635 4734 471920732 471921842 0.000000e+00 1476.0
5 TraesCS4A01G492600 chr6D 82.213 759 112 14 2898 3635 75266043 75266799 2.860000e-177 632.0
6 TraesCS4A01G492600 chr6D 91.192 193 14 3 4776 4966 471921967 471922158 5.590000e-65 259.0
7 TraesCS4A01G492600 chr6B 91.207 1956 128 24 982 2905 716619233 716621176 0.000000e+00 2619.0
8 TraesCS4A01G492600 chr6B 89.883 1196 77 19 3635 4790 716621168 716622359 0.000000e+00 1498.0
9 TraesCS4A01G492600 chr6B 93.844 666 32 7 4965 5623 607742434 607743097 0.000000e+00 994.0
10 TraesCS4A01G492600 chr6B 87.004 731 86 4 2906 3635 587468163 587468885 0.000000e+00 815.0
11 TraesCS4A01G492600 chr6B 89.172 157 15 2 4811 4966 716622564 716622719 1.600000e-45 195.0
12 TraesCS4A01G492600 chrUn 90.108 1951 146 22 987 2905 74820465 74818530 0.000000e+00 2490.0
13 TraesCS4A01G492600 chrUn 89.505 667 65 2 3978 4644 74818163 74817502 0.000000e+00 839.0
14 TraesCS4A01G492600 chrUn 95.440 307 14 0 3635 3941 74818538 74818232 1.820000e-134 490.0
15 TraesCS4A01G492600 chrUn 94.904 157 7 1 4811 4966 74817050 74816894 1.560000e-60 244.0
16 TraesCS4A01G492600 chrUn 94.253 87 5 0 4648 4734 74817461 74817375 3.530000e-27 134.0
17 TraesCS4A01G492600 chrUn 97.143 35 1 0 4752 4786 74817325 74817291 6.080000e-05 60.2
18 TraesCS4A01G492600 chr1B 95.150 969 47 0 2 970 189497800 189498768 0.000000e+00 1530.0
19 TraesCS4A01G492600 chr1B 95.502 667 19 6 4967 5623 525464969 525464304 0.000000e+00 1055.0
20 TraesCS4A01G492600 chr3B 94.320 986 56 0 1 986 412286506 412287491 0.000000e+00 1511.0
21 TraesCS4A01G492600 chr3B 95.770 662 23 3 4967 5623 189059286 189059947 0.000000e+00 1062.0
22 TraesCS4A01G492600 chr3B 95.324 663 22 6 4966 5623 82577836 82577178 0.000000e+00 1044.0
23 TraesCS4A01G492600 chr3B 95.310 661 22 5 4967 5623 163182379 163181724 0.000000e+00 1040.0
24 TraesCS4A01G492600 chr3B 95.166 662 26 4 4965 5623 227732157 227732815 0.000000e+00 1040.0
25 TraesCS4A01G492600 chr3B 94.411 662 29 5 4966 5623 161258368 161259025 0.000000e+00 1011.0
26 TraesCS4A01G492600 chr5B 94.219 986 57 0 1 986 128599930 128598945 0.000000e+00 1506.0
27 TraesCS4A01G492600 chr5B 94.713 662 26 6 4967 5623 205135197 205134540 0.000000e+00 1020.0
28 TraesCS4A01G492600 chr7A 93.813 986 61 0 1 986 140450310 140449325 0.000000e+00 1483.0
29 TraesCS4A01G492600 chr7A 93.813 986 61 0 1 986 275523627 275522642 0.000000e+00 1483.0
30 TraesCS4A01G492600 chr7A 77.123 424 77 11 1024 1445 730428564 730428159 1.580000e-55 228.0
31 TraesCS4A01G492600 chr2B 93.813 986 61 0 1 986 696731196 696732181 0.000000e+00 1483.0
32 TraesCS4A01G492600 chr2B 74.733 1405 265 57 1527 2884 610417516 610418877 3.830000e-151 545.0
33 TraesCS4A01G492600 chr2B 80.816 490 78 13 3686 4171 610419010 610419487 2.470000e-98 370.0
34 TraesCS4A01G492600 chr2B 77.069 423 74 16 1025 1444 610417030 610417432 7.330000e-54 222.0
35 TraesCS4A01G492600 chr1A 93.813 986 61 0 1 986 244376504 244377489 0.000000e+00 1483.0
36 TraesCS4A01G492600 chr1A 78.981 1099 136 50 1793 2853 579216374 579217415 0.000000e+00 662.0
37 TraesCS4A01G492600 chr4B 93.712 986 62 0 1 986 159486562 159487547 0.000000e+00 1478.0
38 TraesCS4A01G492600 chr7B 94.286 665 32 3 4963 5623 675278124 675278786 0.000000e+00 1013.0
39 TraesCS4A01G492600 chr7B 90.798 739 65 3 2897 3635 108287977 108288712 0.000000e+00 985.0
40 TraesCS4A01G492600 chr7B 74.786 1404 266 61 1525 2884 740035198 740033839 8.230000e-153 551.0
41 TraesCS4A01G492600 chr7B 86.283 452 60 2 2905 3355 609725765 609726215 1.820000e-134 490.0
42 TraesCS4A01G492600 chr7B 78.533 736 146 10 2905 3635 406528242 406527514 1.830000e-129 473.0
43 TraesCS4A01G492600 chr7B 91.235 251 19 3 3386 3635 609726214 609726462 6.980000e-89 339.0
44 TraesCS4A01G492600 chr2D 74.457 1934 360 88 1025 2899 518266517 518268375 0.000000e+00 712.0
45 TraesCS4A01G492600 chr2D 80.544 735 129 12 2905 3635 452656621 452657345 2.290000e-153 553.0
46 TraesCS4A01G492600 chr2D 79.713 488 87 10 3686 4171 518268495 518268972 5.390000e-90 342.0
47 TraesCS4A01G492600 chr1D 81.143 875 102 37 2025 2884 482925465 482924639 1.320000e-180 643.0
48 TraesCS4A01G492600 chr1D 86.347 271 32 4 1076 1346 482927314 482927049 1.980000e-74 291.0
49 TraesCS4A01G492600 chr1D 92.593 162 12 0 1664 1825 490938505 490938344 3.390000e-57 233.0
50 TraesCS4A01G492600 chr1D 83.636 220 17 7 1354 1573 490938708 490938508 7.440000e-44 189.0
51 TraesCS4A01G492600 chr2A 79.810 738 134 14 2904 3635 435871626 435870898 1.790000e-144 523.0
52 TraesCS4A01G492600 chr2A 79.108 493 90 12 3686 4172 662341717 662342202 1.510000e-85 327.0
53 TraesCS4A01G492600 chr2A 77.465 426 74 15 1025 1447 662339713 662340119 9.420000e-58 235.0
54 TraesCS4A01G492600 chr5A 82.332 566 95 5 3076 3639 163511835 163512397 2.350000e-133 486.0
55 TraesCS4A01G492600 chr7D 76.887 424 77 12 1023 1445 635586234 635586637 2.640000e-53 220.0


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 TraesCS4A01G492600 chr4A 741544979 741550601 5622 False 10384.000000 10384 100.000000 1 5623 1 chr4A.!!$F2 5622
1 TraesCS4A01G492600 chr4A 69894491 69895476 985 False 1506.000000 1506 94.219000 1 986 1 chr4A.!!$F1 985
2 TraesCS4A01G492600 chr6D 471918859 471922158 3299 False 1451.333333 2619 91.289667 1016 4966 3 chr6D.!!$F2 3950
3 TraesCS4A01G492600 chr6D 75266043 75266799 756 False 632.000000 632 82.213000 2898 3635 1 chr6D.!!$F1 737
4 TraesCS4A01G492600 chr6B 716619233 716622719 3486 False 1437.333333 2619 90.087333 982 4966 3 chr6B.!!$F3 3984
5 TraesCS4A01G492600 chr6B 607742434 607743097 663 False 994.000000 994 93.844000 4965 5623 1 chr6B.!!$F2 658
6 TraesCS4A01G492600 chr6B 587468163 587468885 722 False 815.000000 815 87.004000 2906 3635 1 chr6B.!!$F1 729
7 TraesCS4A01G492600 chrUn 74816894 74820465 3571 True 709.533333 2490 93.558833 987 4966 6 chrUn.!!$R1 3979
8 TraesCS4A01G492600 chr1B 189497800 189498768 968 False 1530.000000 1530 95.150000 2 970 1 chr1B.!!$F1 968
9 TraesCS4A01G492600 chr1B 525464304 525464969 665 True 1055.000000 1055 95.502000 4967 5623 1 chr1B.!!$R1 656
10 TraesCS4A01G492600 chr3B 412286506 412287491 985 False 1511.000000 1511 94.320000 1 986 1 chr3B.!!$F4 985
11 TraesCS4A01G492600 chr3B 189059286 189059947 661 False 1062.000000 1062 95.770000 4967 5623 1 chr3B.!!$F2 656
12 TraesCS4A01G492600 chr3B 82577178 82577836 658 True 1044.000000 1044 95.324000 4966 5623 1 chr3B.!!$R1 657
13 TraesCS4A01G492600 chr3B 163181724 163182379 655 True 1040.000000 1040 95.310000 4967 5623 1 chr3B.!!$R2 656
14 TraesCS4A01G492600 chr3B 227732157 227732815 658 False 1040.000000 1040 95.166000 4965 5623 1 chr3B.!!$F3 658
15 TraesCS4A01G492600 chr3B 161258368 161259025 657 False 1011.000000 1011 94.411000 4966 5623 1 chr3B.!!$F1 657
16 TraesCS4A01G492600 chr5B 128598945 128599930 985 True 1506.000000 1506 94.219000 1 986 1 chr5B.!!$R1 985
17 TraesCS4A01G492600 chr5B 205134540 205135197 657 True 1020.000000 1020 94.713000 4967 5623 1 chr5B.!!$R2 656
18 TraesCS4A01G492600 chr7A 140449325 140450310 985 True 1483.000000 1483 93.813000 1 986 1 chr7A.!!$R1 985
19 TraesCS4A01G492600 chr7A 275522642 275523627 985 True 1483.000000 1483 93.813000 1 986 1 chr7A.!!$R2 985
20 TraesCS4A01G492600 chr2B 696731196 696732181 985 False 1483.000000 1483 93.813000 1 986 1 chr2B.!!$F1 985
21 TraesCS4A01G492600 chr2B 610417030 610419487 2457 False 379.000000 545 77.539333 1025 4171 3 chr2B.!!$F2 3146
22 TraesCS4A01G492600 chr1A 244376504 244377489 985 False 1483.000000 1483 93.813000 1 986 1 chr1A.!!$F1 985
23 TraesCS4A01G492600 chr1A 579216374 579217415 1041 False 662.000000 662 78.981000 1793 2853 1 chr1A.!!$F2 1060
24 TraesCS4A01G492600 chr4B 159486562 159487547 985 False 1478.000000 1478 93.712000 1 986 1 chr4B.!!$F1 985
25 TraesCS4A01G492600 chr7B 675278124 675278786 662 False 1013.000000 1013 94.286000 4963 5623 1 chr7B.!!$F2 660
26 TraesCS4A01G492600 chr7B 108287977 108288712 735 False 985.000000 985 90.798000 2897 3635 1 chr7B.!!$F1 738
27 TraesCS4A01G492600 chr7B 740033839 740035198 1359 True 551.000000 551 74.786000 1525 2884 1 chr7B.!!$R2 1359
28 TraesCS4A01G492600 chr7B 406527514 406528242 728 True 473.000000 473 78.533000 2905 3635 1 chr7B.!!$R1 730
29 TraesCS4A01G492600 chr7B 609725765 609726462 697 False 414.500000 490 88.759000 2905 3635 2 chr7B.!!$F3 730
30 TraesCS4A01G492600 chr2D 452656621 452657345 724 False 553.000000 553 80.544000 2905 3635 1 chr2D.!!$F1 730
31 TraesCS4A01G492600 chr2D 518266517 518268972 2455 False 527.000000 712 77.085000 1025 4171 2 chr2D.!!$F2 3146
32 TraesCS4A01G492600 chr1D 482924639 482927314 2675 True 467.000000 643 83.745000 1076 2884 2 chr1D.!!$R1 1808
33 TraesCS4A01G492600 chr2A 435870898 435871626 728 True 523.000000 523 79.810000 2904 3635 1 chr2A.!!$R1 731
34 TraesCS4A01G492600 chr2A 662339713 662342202 2489 False 281.000000 327 78.286500 1025 4172 2 chr2A.!!$F1 3147
35 TraesCS4A01G492600 chr5A 163511835 163512397 562 False 486.000000 486 82.332000 3076 3639 1 chr5A.!!$F1 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
918 919 1.001764 CATGCCTGGCAACTCCTCA 60.002 57.895 27.24 0.0 43.62 3.86 F
1632 1733 0.605319 TCCGTGTGCCATTCAAGACC 60.605 55.000 0.00 0.0 0.00 3.85 F
2296 3289 0.895100 TTCACAATGCCAGGGCTGTC 60.895 55.000 12.19 0.0 42.51 3.51 F
3113 4220 1.063183 GCTATCCTCCAAGCCTCCAT 58.937 55.000 0.00 0.0 32.40 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 3419 0.803768 CGATCTGAGGGTGCAAGTCG 60.804 60.0 0.0 0.0 0.0 4.18 R
3173 4280 0.456628 GTGGCTAGAGAGGAACCGAC 59.543 60.0 0.0 0.0 0.0 4.79 R
3247 4354 0.463204 CTCATCATCGACAGCACCCT 59.537 55.0 0.0 0.0 0.0 4.34 R
4645 5799 0.248215 GCACACACACAAGCACAGTC 60.248 55.0 0.0 0.0 0.0 3.51 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
74 75 7.362401 CCATTTGAACTTGGTATCCTTCTTCAG 60.362 40.741 0.00 0.00 0.00 3.02
146 147 3.532542 GGTAGTATCCTGCAAGTCCAAC 58.467 50.000 0.00 0.00 0.00 3.77
153 154 3.892284 TCCTGCAAGTCCAACAAAACTA 58.108 40.909 0.00 0.00 0.00 2.24
296 297 3.290710 ACTCACATTTGCTGAACTTGGT 58.709 40.909 0.00 0.00 0.00 3.67
330 331 4.830046 TGTTCTCTGAGCTTCTCAAGTACT 59.170 41.667 0.00 0.00 40.18 2.73
351 352 3.508744 AAACGCAAATGCTCCTTATGG 57.491 42.857 3.63 0.00 39.32 2.74
473 474 1.329256 ACAGGTGCGTTAGTCAGACT 58.671 50.000 8.50 8.50 0.00 3.24
530 531 2.369532 TGGTGGTAAAAGCCGTCTTAGT 59.630 45.455 0.00 0.00 31.02 2.24
763 764 3.078837 GGTGAAGAACTTGGGCGAATAA 58.921 45.455 0.00 0.00 0.00 1.40
791 792 7.993758 GCCTTTATCCAGTAACTCCTTAATCTT 59.006 37.037 0.00 0.00 0.00 2.40
884 885 6.187480 GCAAAAGCTCAATCAAAAACTCAAC 58.813 36.000 0.00 0.00 0.00 3.18
918 919 1.001764 CATGCCTGGCAACTCCTCA 60.002 57.895 27.24 0.00 43.62 3.86
927 928 2.280628 GGCAACTCCTCAGGAAATACG 58.719 52.381 0.00 0.00 0.00 3.06
934 935 1.831736 CCTCAGGAAATACGTCAGGGT 59.168 52.381 0.00 0.00 0.00 4.34
950 951 4.162320 GTCAGGGTAATCCTTCATCACTGA 59.838 45.833 0.00 0.00 45.47 3.41
974 975 1.002868 CCTCCTGCACAACTCCTGG 60.003 63.158 0.00 0.00 0.00 4.45
979 980 1.072331 CCTGCACAACTCCTGGTAAGT 59.928 52.381 0.00 0.00 0.00 2.24
1038 1039 1.949257 CCGTTGCAGGTTTCAGGAC 59.051 57.895 0.00 0.00 0.00 3.85
1069 1070 0.838987 GAAGGGGTGGGGTGACACTA 60.839 60.000 5.39 0.00 41.09 2.74
1218 1219 4.515567 GGTTACTTTGGTCAAGAGAAGGTG 59.484 45.833 0.00 0.00 36.21 4.00
1230 1231 2.524148 AAGGTGCTTGGGTTGCCC 60.524 61.111 0.00 0.00 45.71 5.36
1267 1273 7.812191 GTCAGGTACAGTGATCATTATCTCATC 59.188 40.741 0.00 0.00 32.93 2.92
1498 1599 2.039831 GTCCAGGGAGGGGGCATA 60.040 66.667 0.00 0.00 38.24 3.14
1521 1622 3.800863 GCTCCTCGCTCGTGTCGA 61.801 66.667 4.49 4.49 35.14 4.20
1522 1623 3.102985 CTCCTCGCTCGTGTCGAT 58.897 61.111 0.00 0.00 34.61 3.59
1523 1624 1.010574 CTCCTCGCTCGTGTCGATC 60.011 63.158 0.00 0.00 34.61 3.69
1574 1675 4.707988 CACCAAGTGCAACGTTGG 57.292 55.556 28.33 14.92 44.96 3.77
1596 1697 2.023414 TTGAACCGGTCGAGCACACT 62.023 55.000 8.04 0.00 0.00 3.55
1632 1733 0.605319 TCCGTGTGCCATTCAAGACC 60.605 55.000 0.00 0.00 0.00 3.85
1862 1966 5.065914 CCAGACATGGTCATCGGAAATTAT 58.934 41.667 0.00 0.00 42.17 1.28
2007 2135 2.086610 ACCAACAGGGAACAATTGCT 57.913 45.000 5.05 0.00 41.15 3.91
2039 3013 4.583489 TGAGAAGACAAAGTACGAGGACTT 59.417 41.667 0.00 0.00 41.50 3.01
2089 3063 3.618690 AGTATCACTTCTCCTGCCAAC 57.381 47.619 0.00 0.00 0.00 3.77
2148 3122 1.032794 TCATCGCTAGCACCTACCAG 58.967 55.000 16.45 0.00 0.00 4.00
2174 3148 2.609747 AGCCAGAAGGTCAGTAACTCA 58.390 47.619 0.00 0.00 37.19 3.41
2181 3155 5.927115 CAGAAGGTCAGTAACTCAGTAAACC 59.073 44.000 0.00 0.00 0.00 3.27
2186 3160 5.695363 GGTCAGTAACTCAGTAAACCAAGAC 59.305 44.000 0.00 0.00 0.00 3.01
2189 3163 6.042781 TCAGTAACTCAGTAAACCAAGACCAT 59.957 38.462 0.00 0.00 0.00 3.55
2190 3164 6.369065 CAGTAACTCAGTAAACCAAGACCATC 59.631 42.308 0.00 0.00 0.00 3.51
2191 3165 5.568620 AACTCAGTAAACCAAGACCATCT 57.431 39.130 0.00 0.00 0.00 2.90
2296 3289 0.895100 TTCACAATGCCAGGGCTGTC 60.895 55.000 12.19 0.00 42.51 3.51
2390 3385 6.531948 CCGTTTACTTTCCATTCACACAAAAA 59.468 34.615 0.00 0.00 0.00 1.94
2397 3411 3.125316 CCATTCACACAAAAACAGGCTG 58.875 45.455 14.16 14.16 0.00 4.85
2405 3419 1.115326 AAAAACAGGCTGGGCTGACC 61.115 55.000 26.72 0.00 40.81 4.02
2700 3771 2.297895 CCTGGTCATCGTTGGGGGA 61.298 63.158 0.00 0.00 0.00 4.81
2712 3783 2.204090 GGGGGACTCCTGGAACCA 60.204 66.667 17.44 0.00 35.33 3.67
2738 3809 3.978217 CAGTCAAACGACAGAGAAGAGAC 59.022 47.826 0.00 0.00 35.75 3.36
2758 3829 2.169352 ACCGAGGAGATCAACAAGATGG 59.831 50.000 0.00 0.00 37.00 3.51
2774 3845 2.508716 AGATGGACAGCTTGATGGACAT 59.491 45.455 0.00 0.00 0.00 3.06
2970 4051 5.331069 GGGTAGGGAGCAGTATATACAAGA 58.669 45.833 15.18 0.00 0.00 3.02
2976 4057 2.621998 AGCAGTATATACAAGACCGCGT 59.378 45.455 15.18 0.00 0.00 6.01
2991 4072 1.495951 GCGTTCGCGGTTCTGAAAT 59.504 52.632 6.13 0.00 41.67 2.17
3017 4107 7.286316 TGAGAAAAGCAAAGAGAAGGAAAAGAT 59.714 33.333 0.00 0.00 0.00 2.40
3019 4125 9.136323 AGAAAAGCAAAGAGAAGGAAAAGATTA 57.864 29.630 0.00 0.00 0.00 1.75
3031 4137 4.293901 AGGAAAAGATTACAGGGCCCTTAA 59.706 41.667 26.10 23.00 0.00 1.85
3096 4203 1.589716 GCAGACATTTTGCTCCCGCT 61.590 55.000 0.00 0.00 38.51 5.52
3113 4220 1.063183 GCTATCCTCCAAGCCTCCAT 58.937 55.000 0.00 0.00 32.40 3.41
3124 4231 2.851102 CCTCCATGGATCCCCGCT 60.851 66.667 16.63 0.00 38.35 5.52
3132 4239 3.157252 GATCCCCGCTCTGCCTGA 61.157 66.667 0.00 0.00 0.00 3.86
3144 4251 2.522680 GCCTGAATGATGGCCCCC 60.523 66.667 0.00 0.00 43.11 5.40
3239 4346 2.821546 CGACCTGATTCCTTTGCGATA 58.178 47.619 0.00 0.00 0.00 2.92
3240 4347 3.393800 CGACCTGATTCCTTTGCGATAT 58.606 45.455 0.00 0.00 0.00 1.63
3245 4352 4.214971 CCTGATTCCTTTGCGATATTCTGG 59.785 45.833 0.00 0.00 0.00 3.86
3247 4354 2.708216 TCCTTTGCGATATTCTGGCA 57.292 45.000 0.00 0.00 36.74 4.92
3265 4372 0.176449 CAGGGTGCTGTCGATGATGA 59.824 55.000 0.00 0.00 0.00 2.92
3267 4374 0.461548 GGGTGCTGTCGATGATGAGA 59.538 55.000 0.00 0.00 0.00 3.27
3417 4524 2.287368 GGTTTCAAGGTTTCGAACGCAT 60.287 45.455 0.00 0.00 0.00 4.73
3543 4654 1.340991 GCCCAGGCTTTCCAGAACATA 60.341 52.381 0.08 0.00 38.26 2.29
3560 4671 7.359849 CCAGAACATAGTTGCATAATCTGATCG 60.360 40.741 0.00 0.00 36.11 3.69
3727 4838 3.006940 GCATTTGGACTAACGGTCATCA 58.993 45.455 0.00 0.00 46.16 3.07
3753 4864 4.892965 AACTGCGGGCTGCCAACA 62.893 61.111 22.05 16.24 45.60 3.33
3852 4963 0.107945 AGGAGGCAAGCGACAAGATC 60.108 55.000 0.00 0.00 0.00 2.75
3955 5090 4.649674 AGTGGTACCGTACAATCATCATCT 59.350 41.667 7.57 0.00 0.00 2.90
3994 5138 9.727627 GGATAATTATGCTTCTTCTTCACAAAG 57.272 33.333 9.54 0.00 0.00 2.77
4111 5258 3.576550 GACTCTGAACAAGGAAGAGAGGT 59.423 47.826 5.95 0.00 39.91 3.85
4128 5275 2.436173 GAGGTAGGCCAAACAGCTCTAT 59.564 50.000 5.01 0.00 37.19 1.98
4180 5327 3.434984 GCAGCTGGTTAGTTCAGAAGAAG 59.565 47.826 17.12 0.00 33.63 2.85
4229 5381 3.324556 CCAACCCCATTTTCACTGATGTT 59.675 43.478 0.00 0.00 0.00 2.71
4230 5382 4.559153 CAACCCCATTTTCACTGATGTTC 58.441 43.478 0.00 0.00 0.00 3.18
4231 5383 4.118168 ACCCCATTTTCACTGATGTTCT 57.882 40.909 0.00 0.00 0.00 3.01
4232 5384 5.255397 ACCCCATTTTCACTGATGTTCTA 57.745 39.130 0.00 0.00 0.00 2.10
4247 5399 9.640963 ACTGATGTTCTACATTTGTTAGTACTC 57.359 33.333 0.00 0.00 39.27 2.59
4263 5415 8.698210 TGTTAGTACTCTTTTCAGGTAAAGACA 58.302 33.333 0.00 0.00 38.78 3.41
4272 5424 4.781775 TCAGGTAAAGACAGTCCCAAAA 57.218 40.909 0.00 0.00 0.00 2.44
4273 5425 4.457466 TCAGGTAAAGACAGTCCCAAAAC 58.543 43.478 0.00 0.00 0.00 2.43
4314 5466 3.291101 TACGACAGGAAGCACGGCC 62.291 63.158 0.00 0.00 0.00 6.13
4366 5518 1.746615 CAAGTGTGCCCGCTGCTAT 60.747 57.895 0.00 0.00 42.00 2.97
4428 5580 1.060842 TGACCGTTTGTTGTTTCGACG 59.939 47.619 0.00 0.00 0.00 5.12
4429 5581 3.136800 CCGTTTGTTGTTTCGACGG 57.863 52.632 0.00 0.00 45.86 4.79
4431 5583 1.448722 CGTTTGTTGTTTCGACGGTG 58.551 50.000 0.00 0.00 0.00 4.94
4469 5621 3.513515 GAGGATTCAGAGGTGAGAGTTGT 59.486 47.826 0.00 0.00 32.98 3.32
4554 5708 9.955208 TGATGAATATCTGAATAATGTGTTTGC 57.045 29.630 0.00 0.00 34.31 3.68
4562 5716 4.082300 TGAATAATGTGTTTGCGCAGGATT 60.082 37.500 11.31 8.26 38.63 3.01
4607 5761 0.538977 TCCCGACGTCCAACTTCTCT 60.539 55.000 10.58 0.00 0.00 3.10
4636 5790 4.584325 TGCAGCTTAAAGTGAAGACCAAAT 59.416 37.500 0.00 0.00 0.00 2.32
4638 5792 6.434028 TGCAGCTTAAAGTGAAGACCAAATAT 59.566 34.615 0.00 0.00 0.00 1.28
4647 5801 8.738645 AAGTGAAGACCAAATATCATAAGGAC 57.261 34.615 0.00 0.00 0.00 3.85
4651 5842 7.770433 TGAAGACCAAATATCATAAGGACTGTG 59.230 37.037 0.00 0.00 0.00 3.66
4653 5844 6.006275 ACCAAATATCATAAGGACTGTGCT 57.994 37.500 0.00 0.00 0.00 4.40
4718 5909 5.169992 ACTGTCCATGATGATTGTGAGAA 57.830 39.130 0.00 0.00 0.00 2.87
4747 5956 1.023513 GTGTGAGCCCTGCACTCATC 61.024 60.000 8.57 4.32 45.40 2.92
4790 6019 7.299586 GCATCATGCAAAAGCAAGAAAAATAA 58.700 30.769 4.20 0.00 44.26 1.40
4791 6020 7.804129 GCATCATGCAAAAGCAAGAAAAATAAA 59.196 29.630 4.20 0.00 44.26 1.40
4793 6022 7.354257 TCATGCAAAAGCAAGAAAAATAAAGC 58.646 30.769 0.00 0.00 0.00 3.51
4794 6023 6.674694 TGCAAAAGCAAGAAAAATAAAGCA 57.325 29.167 0.00 0.00 0.00 3.91
4796 6025 7.188157 TGCAAAAGCAAGAAAAATAAAGCAAG 58.812 30.769 0.00 0.00 0.00 4.01
4797 6026 7.148272 TGCAAAAGCAAGAAAAATAAAGCAAGT 60.148 29.630 0.00 0.00 0.00 3.16
4874 6331 9.313323 CATTTACAACATAACAAAGTAGACACG 57.687 33.333 0.00 0.00 0.00 4.49
4912 6369 5.104941 AGCAAACATAGACCAGCATAGTACA 60.105 40.000 0.00 0.00 0.00 2.90
4919 6376 0.460109 CCAGCATAGTACAGCGCACA 60.460 55.000 11.47 0.00 35.48 4.57
5113 6572 4.363990 CCAGTCTCACGGTGCGCT 62.364 66.667 9.73 0.00 0.00 5.92
5186 6650 2.351726 GACAAAGTGCGCCATTACTAGG 59.648 50.000 4.18 0.00 0.00 3.02
5219 6683 2.972505 CGCACGGCCAAGACAGTT 60.973 61.111 2.24 0.00 0.00 3.16
5326 6797 0.968405 AATGGCGCACTTTTCCACAT 59.032 45.000 10.83 0.00 31.94 3.21
5501 6974 2.221299 GCCCACCTACCCACTCACA 61.221 63.158 0.00 0.00 0.00 3.58
5540 7014 1.573108 CACCTCCTCCTCCAAGCTTA 58.427 55.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.566197 AGTTCAAATGGACTGAAGAATGTC 57.434 37.500 0.00 0.00 33.56 3.06
146 147 4.822026 AGTTGGAGAGATCCGTAGTTTTG 58.178 43.478 0.00 0.00 0.00 2.44
296 297 6.782082 AGCTCAGAGAACATCAGTTATACA 57.218 37.500 0.00 0.00 38.30 2.29
330 331 4.013728 ACCATAAGGAGCATTTGCGTTTA 58.986 39.130 0.00 0.00 41.84 2.01
351 352 7.155328 TGGTCTACTCAAAGAATGAAGAAGAC 58.845 38.462 0.00 0.00 38.82 3.01
454 455 1.329256 AGTCTGACTAACGCACCTGT 58.671 50.000 8.91 0.00 0.00 4.00
530 531 9.373450 AGTTGAAGATTAGAGAGCAGGATATAA 57.627 33.333 0.00 0.00 0.00 0.98
763 764 5.780958 AAGGAGTTACTGGATAAAGGCTT 57.219 39.130 0.00 0.00 0.00 4.35
791 792 8.796475 CACAAGATTTGGAGGAAATTAAGAAGA 58.204 33.333 0.00 0.00 34.18 2.87
884 885 0.319040 CATGCCACCGGATAGAGACG 60.319 60.000 9.46 0.00 0.00 4.18
918 919 4.296056 AGGATTACCCTGACGTATTTCCT 58.704 43.478 0.00 0.00 45.61 3.36
934 935 7.015682 GGAGGAAGTATCAGTGATGAAGGATTA 59.984 40.741 16.15 0.00 0.00 1.75
950 951 2.237392 GGAGTTGTGCAGGAGGAAGTAT 59.763 50.000 0.00 0.00 0.00 2.12
974 975 8.349983 TCGGTCGGTTAGGTATAAATTACTTAC 58.650 37.037 0.00 0.00 0.00 2.34
979 980 7.523293 TCATCGGTCGGTTAGGTATAAATTA 57.477 36.000 0.00 0.00 0.00 1.40
991 992 2.814280 GACCATATCATCGGTCGGTT 57.186 50.000 0.00 0.00 42.19 4.44
1038 1039 0.921256 ACCCCTTCTCCAATCCCCAG 60.921 60.000 0.00 0.00 0.00 4.45
1069 1070 3.070734 AGTGTTTCTCTGCATGTCTCAGT 59.929 43.478 0.00 0.00 33.48 3.41
1230 1231 2.188829 TACCTGACCGCCGGTATCG 61.189 63.158 9.73 0.89 35.25 2.92
1267 1273 9.449719 GTTGATTCAGGGTTATAATATACCAGG 57.550 37.037 0.00 0.00 36.10 4.45
1297 1303 4.171754 GGCTTCTGTTTCAAGCATGAATC 58.828 43.478 5.03 5.54 46.94 2.52
1516 1617 2.984471 GTCTTGTTAACTGCGATCGACA 59.016 45.455 21.57 15.18 0.00 4.35
1517 1618 3.243336 AGTCTTGTTAACTGCGATCGAC 58.757 45.455 21.57 10.98 0.00 4.20
1520 1621 5.232414 GGTATGAGTCTTGTTAACTGCGATC 59.768 44.000 7.22 1.03 0.00 3.69
1521 1622 5.109903 GGTATGAGTCTTGTTAACTGCGAT 58.890 41.667 7.22 0.00 0.00 4.58
1522 1623 4.491676 GGTATGAGTCTTGTTAACTGCGA 58.508 43.478 7.22 0.00 0.00 5.10
1523 1624 3.303495 CGGTATGAGTCTTGTTAACTGCG 59.697 47.826 7.22 0.00 0.00 5.18
1574 1675 3.119096 GCTCGACCGGTTCAAGCC 61.119 66.667 20.23 2.50 0.00 4.35
1596 1697 2.092968 ACGGAGGATGCTTGAATGCTTA 60.093 45.455 0.00 0.00 0.00 3.09
1632 1733 3.004106 GGCGAAGATCTTTCCCATCATTG 59.996 47.826 9.87 0.00 0.00 2.82
1752 1854 1.511850 TCAGTGCCACATTCAGTTCG 58.488 50.000 0.00 0.00 0.00 3.95
1856 1960 8.512138 GCTACTAAATTGCCATCGGTATAATTT 58.488 33.333 0.00 0.00 35.72 1.82
1862 1966 4.409718 TGCTACTAAATTGCCATCGGTA 57.590 40.909 0.00 0.00 0.00 4.02
1972 2082 5.437289 TGTTGGTTGTGATGTCAGATTTC 57.563 39.130 0.00 0.00 0.00 2.17
2007 2135 4.965814 ACTTTGTCTTCTCAAGAGCATGA 58.034 39.130 0.00 0.00 38.41 3.07
2039 3013 5.721480 TCCATTTCTCTCCACTTGACATCTA 59.279 40.000 0.00 0.00 0.00 1.98
2089 3063 1.863454 GGCGATCATGTCAGCAGTAAG 59.137 52.381 10.15 0.00 0.00 2.34
2148 3122 3.636153 ACTGACCTTCTGGCTATTTCC 57.364 47.619 0.00 0.00 36.63 3.13
2186 3160 0.907486 TGAGAGACAGGGCAAGATGG 59.093 55.000 0.00 0.00 0.00 3.51
2189 3163 1.978473 GCTGAGAGACAGGGCAAGA 59.022 57.895 0.00 0.00 45.82 3.02
2190 3164 4.613929 GCTGAGAGACAGGGCAAG 57.386 61.111 0.00 0.00 45.82 4.01
2195 3169 1.065401 GATGAGTCGCTGAGAGACAGG 59.935 57.143 18.26 0.00 45.82 4.00
2397 3411 3.050275 GTGCAAGTCGGTCAGCCC 61.050 66.667 0.00 0.00 0.00 5.19
2405 3419 0.803768 CGATCTGAGGGTGCAAGTCG 60.804 60.000 0.00 0.00 0.00 4.18
2700 3771 1.625818 GACTGTGATGGTTCCAGGAGT 59.374 52.381 0.00 0.00 0.00 3.85
2712 3783 4.038042 TCTTCTCTGTCGTTTGACTGTGAT 59.962 41.667 7.54 0.00 45.70 3.06
2738 3809 2.432146 TCCATCTTGTTGATCTCCTCGG 59.568 50.000 0.00 0.00 32.05 4.63
2758 3829 2.939103 GGTACATGTCCATCAAGCTGTC 59.061 50.000 0.00 0.00 0.00 3.51
2774 3845 0.976641 CTGTCCCTTGAGCTGGTACA 59.023 55.000 0.00 0.00 0.00 2.90
2827 3905 1.301401 GGTACAGCTCACCGTTGCA 60.301 57.895 0.00 0.00 0.00 4.08
2936 4016 5.017431 ACTGCTCCCTACCCCATAATATAGA 59.983 44.000 0.00 0.00 0.00 1.98
2937 4017 5.281314 ACTGCTCCCTACCCCATAATATAG 58.719 45.833 0.00 0.00 0.00 1.31
2976 4057 2.448926 TCTCATTTCAGAACCGCGAA 57.551 45.000 8.23 0.00 0.00 4.70
2985 4066 6.862090 CCTTCTCTTTGCTTTTCTCATTTCAG 59.138 38.462 0.00 0.00 0.00 3.02
2991 4072 6.603201 TCTTTTCCTTCTCTTTGCTTTTCTCA 59.397 34.615 0.00 0.00 0.00 3.27
3037 4143 1.215382 CGTGAGAGATCGCCCAACA 59.785 57.895 0.00 0.00 0.00 3.33
3096 4203 1.061424 TCCATGGAGGCTTGGAGGATA 60.061 52.381 11.44 0.00 37.10 2.59
3113 4220 4.804420 AGGCAGAGCGGGGATCCA 62.804 66.667 15.23 0.00 0.00 3.41
3144 4251 1.084370 AGAAGAAAATCGCCGAGCCG 61.084 55.000 0.00 0.00 0.00 5.52
3171 4278 1.031029 GGCTAGAGAGGAACCGACGT 61.031 60.000 0.00 0.00 0.00 4.34
3173 4280 0.456628 GTGGCTAGAGAGGAACCGAC 59.543 60.000 0.00 0.00 0.00 4.79
3213 4320 1.270907 AAGGAATCAGGTCGCTCACT 58.729 50.000 0.00 0.00 0.00 3.41
3239 4346 1.001641 GACAGCACCCTGCCAGAAT 60.002 57.895 0.00 0.00 46.52 2.40
3240 4347 2.431683 GACAGCACCCTGCCAGAA 59.568 61.111 0.00 0.00 46.52 3.02
3245 4352 1.153289 ATCATCGACAGCACCCTGC 60.153 57.895 0.00 0.00 45.46 4.85
3247 4354 0.463204 CTCATCATCGACAGCACCCT 59.537 55.000 0.00 0.00 0.00 4.34
3375 4482 2.046507 GTGCACCTCCTCTGGCAG 60.047 66.667 8.58 8.58 36.86 4.85
3384 4491 1.876156 CTTGAAACCTCAGTGCACCTC 59.124 52.381 14.63 0.00 31.69 3.85
3417 4524 3.728845 GAATGACTATTTCTGCCCGCTA 58.271 45.455 0.00 0.00 0.00 4.26
3543 4654 4.285517 AGGATCCGATCAGATTATGCAACT 59.714 41.667 5.98 0.00 0.00 3.16
3560 4671 4.162690 AGTTCGCCGGCAGGATCC 62.163 66.667 28.98 2.48 41.02 3.36
3570 4681 2.882742 CTTACAAGCTTCAGTTCGCC 57.117 50.000 0.00 0.00 0.00 5.54
3727 4838 2.436646 CCCGCAGTTCATCGCCTT 60.437 61.111 0.00 0.00 0.00 4.35
3753 4864 2.009774 CCTCCTTGATTTGTCGCGAAT 58.990 47.619 12.06 0.00 0.00 3.34
4007 5151 7.169308 ACGTGTAACTAAAATCACAGACAAGAG 59.831 37.037 0.00 0.00 31.75 2.85
4111 5258 4.286707 TGTAGATAGAGCTGTTTGGCCTA 58.713 43.478 3.32 0.00 0.00 3.93
4128 5275 6.493802 ACTGAAGGTTGTAGAACATCTGTAGA 59.506 38.462 14.18 0.00 33.63 2.59
4180 5327 1.226945 GGTGTTGGTGTTGCACTGC 60.227 57.895 0.00 0.00 34.40 4.40
4229 5381 9.706691 CCTGAAAAGAGTACTAACAAATGTAGA 57.293 33.333 0.00 0.00 0.00 2.59
4230 5382 9.490379 ACCTGAAAAGAGTACTAACAAATGTAG 57.510 33.333 0.00 0.00 0.00 2.74
4232 5384 9.841295 TTACCTGAAAAGAGTACTAACAAATGT 57.159 29.630 0.00 0.00 0.00 2.71
4242 5394 6.645827 GGACTGTCTTTACCTGAAAAGAGTAC 59.354 42.308 7.85 0.00 44.09 2.73
4247 5399 4.714632 TGGGACTGTCTTTACCTGAAAAG 58.285 43.478 7.85 0.00 37.73 2.27
4272 5424 3.223589 GCGGGTTGTTTGCCCAGT 61.224 61.111 1.07 0.00 46.40 4.00
4273 5425 3.222855 TGCGGGTTGTTTGCCCAG 61.223 61.111 1.07 0.00 46.40 4.45
4279 5431 3.479127 TAGGCCGTGCGGGTTGTTT 62.479 57.895 12.82 0.00 38.44 2.83
4363 5515 7.543868 CCGCTATCTCCTCAGTAAATTTCATAG 59.456 40.741 0.00 0.00 0.00 2.23
4366 5518 5.453339 CCCGCTATCTCCTCAGTAAATTTCA 60.453 44.000 0.00 0.00 0.00 2.69
4431 5583 4.742201 TCGTCTGCGGCCTTCTGC 62.742 66.667 0.00 0.00 44.80 4.26
4469 5621 2.203470 TGCAGCTTGATGATTGGTGA 57.797 45.000 0.00 0.00 0.00 4.02
4497 5649 4.730657 CAAATGTGACCTGATGCTTCTTC 58.269 43.478 0.88 0.00 0.00 2.87
4562 5716 2.571757 CCGAGTAAGCTGGTCGCA 59.428 61.111 7.02 0.00 42.61 5.10
4607 5761 3.701205 TCACTTTAAGCTGCATCCTGA 57.299 42.857 1.02 0.00 0.00 3.86
4636 5790 5.178061 CACACAAGCACAGTCCTTATGATA 58.822 41.667 0.00 0.00 0.00 2.15
4638 5792 3.181455 ACACACAAGCACAGTCCTTATGA 60.181 43.478 0.00 0.00 0.00 2.15
4644 5798 0.378257 CACACACACAAGCACAGTCC 59.622 55.000 0.00 0.00 0.00 3.85
4645 5799 0.248215 GCACACACACAAGCACAGTC 60.248 55.000 0.00 0.00 0.00 3.51
4646 5800 1.656818 GGCACACACACAAGCACAGT 61.657 55.000 0.00 0.00 0.00 3.55
4647 5801 1.064621 GGCACACACACAAGCACAG 59.935 57.895 0.00 0.00 0.00 3.66
4718 5909 2.756760 CAGGGCTCACACTTTGCATTAT 59.243 45.455 0.00 0.00 0.00 1.28
4790 6019 7.259290 TGAAATCTCGTTTCTAAACTTGCTT 57.741 32.000 4.24 0.00 45.22 3.91
4791 6020 6.861065 TGAAATCTCGTTTCTAAACTTGCT 57.139 33.333 4.24 0.00 45.22 3.91
4793 6022 7.355778 AGCTTGAAATCTCGTTTCTAAACTTG 58.644 34.615 4.24 0.00 45.22 3.16
4794 6023 7.308049 GGAGCTTGAAATCTCGTTTCTAAACTT 60.308 37.037 4.24 0.00 45.22 2.66
4796 6025 6.073222 TGGAGCTTGAAATCTCGTTTCTAAAC 60.073 38.462 0.00 0.00 45.22 2.01
4797 6026 5.995282 TGGAGCTTGAAATCTCGTTTCTAAA 59.005 36.000 0.00 0.00 45.22 1.85
4869 6326 3.119602 TGCTGAAGTACCATCTACGTGTC 60.120 47.826 0.00 0.00 0.00 3.67
4874 6331 7.222999 GTCTATGTTTGCTGAAGTACCATCTAC 59.777 40.741 0.00 0.00 0.00 2.59
4974 6432 9.453830 AATCAGTCCTATCTATAACCCTTTTCT 57.546 33.333 0.00 0.00 0.00 2.52
4983 6441 9.547279 TGCCATTAGAATCAGTCCTATCTATAA 57.453 33.333 0.00 0.00 0.00 0.98
5016 6474 1.475403 AGTAGTGGCGCACTGTCTAT 58.525 50.000 18.70 0.00 45.01 1.98
5142 6602 5.994668 TCATCATGCGCCATTAGTTTGTATA 59.005 36.000 4.18 0.00 0.00 1.47
5186 6650 2.787680 CGTGCGCCATTACTAGTTCTAC 59.212 50.000 4.18 0.00 0.00 2.59
5326 6797 7.737972 AAACATATGTATACTAATGGCGCAA 57.262 32.000 10.83 0.00 0.00 4.85
5358 6831 6.419413 CGCCATTAGTACTTTTTGCAGAAAAA 59.581 34.615 0.00 0.17 38.47 1.94
5501 6974 3.054065 GTGGAGAGAATGAAGTGGGGAAT 60.054 47.826 0.00 0.00 0.00 3.01
5540 7014 2.841988 GGAGGAGGCAGCCGAGAT 60.842 66.667 5.55 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.