Multiple sequence alignment - TraesCS5B01G503000

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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 TraesCS5B01G503000 chr5B 100.000 5376 0 0 1 5376 669730121 669735496 0.000000e+00 9928
1 TraesCS5B01G503000 chr5B 97.388 536 11 1 4841 5376 507221906 507221374 0.000000e+00 909
2 TraesCS5B01G503000 chr7D 91.786 2435 145 26 1 2398 52490672 52493088 0.000000e+00 3338
3 TraesCS5B01G503000 chr7D 89.564 1284 121 8 3559 4837 15224985 15226260 0.000000e+00 1616
4 TraesCS5B01G503000 chr7D 93.253 415 26 2 2374 2787 75333119 75333532 1.280000e-170 610
5 TraesCS5B01G503000 chr2D 90.025 2406 178 28 3 2371 16922285 16919905 0.000000e+00 3057
6 TraesCS5B01G503000 chr2D 89.583 1296 115 13 3556 4842 21212299 21213583 0.000000e+00 1628
7 TraesCS5B01G503000 chr2D 93.073 794 45 6 2783 3576 16919411 16918628 0.000000e+00 1153
8 TraesCS5B01G503000 chr2D 91.787 414 29 4 2374 2785 221292355 221292765 6.040000e-159 571
9 TraesCS5B01G503000 chr1A 92.260 2080 140 14 2771 4841 38344449 38342382 0.000000e+00 2929
10 TraesCS5B01G503000 chr1A 88.896 1558 131 24 3 1557 38347227 38345709 0.000000e+00 1881
11 TraesCS5B01G503000 chr1A 94.409 787 36 4 1591 2371 38345705 38344921 0.000000e+00 1203
12 TraesCS5B01G503000 chr1A 90.820 817 51 12 1343 2144 576696661 576695854 0.000000e+00 1072
13 TraesCS5B01G503000 chr1A 92.233 412 25 3 2374 2785 38344874 38344470 1.300000e-160 577
14 TraesCS5B01G503000 chr2B 90.892 2086 154 23 2756 4838 51798280 51796228 0.000000e+00 2767
15 TraesCS5B01G503000 chr2B 88.457 1646 158 14 1 1628 51802604 51800973 0.000000e+00 1958
16 TraesCS5B01G503000 chr2B 87.123 1491 160 21 30 1505 723976940 723978413 0.000000e+00 1661
17 TraesCS5B01G503000 chr2B 94.286 840 39 3 1537 2367 723978411 723979250 0.000000e+00 1277
18 TraesCS5B01G503000 chr6A 90.931 2062 171 8 2783 4842 193177359 193175312 0.000000e+00 2758
19 TraesCS5B01G503000 chr6A 89.774 1281 118 9 3559 4832 441294615 441293341 0.000000e+00 1628
20 TraesCS5B01G503000 chr4A 90.552 2064 162 16 2785 4843 605879882 605881917 0.000000e+00 2700
21 TraesCS5B01G503000 chr4A 91.304 1288 101 4 3556 4841 294601268 294602546 0.000000e+00 1748
22 TraesCS5B01G503000 chr4A 91.587 416 29 2 2374 2785 605879433 605879846 2.170000e-158 569
23 TraesCS5B01G503000 chr4A 91.155 407 33 1 1363 1769 605878654 605879057 2.830000e-152 549
24 TraesCS5B01G503000 chr3A 88.760 1557 134 23 3 1556 732955209 732953691 0.000000e+00 1868
25 TraesCS5B01G503000 chr3A 92.572 1104 73 6 2771 3872 732952428 732951332 0.000000e+00 1576
26 TraesCS5B01G503000 chr3A 94.917 787 34 2 1591 2371 732953686 732952900 0.000000e+00 1227
27 TraesCS5B01G503000 chr3A 94.395 785 40 1 1591 2371 101775648 101776432 0.000000e+00 1203
28 TraesCS5B01G503000 chr3A 92.095 797 53 4 2780 3576 101776921 101777707 0.000000e+00 1114
29 TraesCS5B01G503000 chr3A 91.940 794 55 3 2783 3576 297823372 297822588 0.000000e+00 1103
30 TraesCS5B01G503000 chr3A 85.826 642 69 11 933 1557 297837477 297836841 0.000000e+00 662
31 TraesCS5B01G503000 chr3A 92.029 414 29 3 2374 2785 101776479 101776890 3.610000e-161 579
32 TraesCS5B01G503000 chr2A 88.469 1561 136 22 3 1557 671215379 671216901 0.000000e+00 1845
33 TraesCS5B01G503000 chr2A 92.121 863 61 5 2771 3631 671218164 671219021 0.000000e+00 1210
34 TraesCS5B01G503000 chr2A 94.289 788 38 2 1591 2371 671216905 671217692 0.000000e+00 1199
35 TraesCS5B01G503000 chr2A 91.587 416 28 6 2374 2785 547852437 547852849 7.810000e-158 568
36 TraesCS5B01G503000 chr7B 90.994 1288 109 5 3557 4842 710130406 710129124 0.000000e+00 1729
37 TraesCS5B01G503000 chr7B 90.980 1286 110 4 3557 4840 710107700 710106419 0.000000e+00 1727
38 TraesCS5B01G503000 chr7B 90.388 1290 114 10 3557 4842 710047751 710046468 0.000000e+00 1687
39 TraesCS5B01G503000 chr7B 88.830 1128 78 19 1043 2145 747463023 747464127 0.000000e+00 1341
40 TraesCS5B01G503000 chr7B 87.988 1024 93 13 15 1034 710113765 710112768 0.000000e+00 1182
41 TraesCS5B01G503000 chr7B 96.828 536 14 1 4841 5376 610202281 610201749 0.000000e+00 893
42 TraesCS5B01G503000 chr7B 93.431 411 27 0 2374 2784 21654798 21655208 1.280000e-170 610
43 TraesCS5B01G503000 chr7B 84.317 644 62 16 1043 1665 710111283 710110658 1.290000e-165 593
44 TraesCS5B01G503000 chr7B 84.031 645 62 17 1043 1665 710133988 710133363 2.790000e-162 582
45 TraesCS5B01G503000 chr7B 83.851 644 65 16 1043 1665 710122382 710121757 1.300000e-160 577
46 TraesCS5B01G503000 chr7B 83.066 561 60 15 1043 1586 710080841 710080299 1.350000e-130 477
47 TraesCS5B01G503000 chr7A 85.152 1549 154 31 3 1529 128297778 128299272 0.000000e+00 1517
48 TraesCS5B01G503000 chr7A 90.568 827 55 12 1332 2144 650510714 650509897 0.000000e+00 1074
49 TraesCS5B01G503000 chr7A 97.201 536 12 1 4841 5376 656988340 656987808 0.000000e+00 904
50 TraesCS5B01G503000 chr7A 96.455 536 18 1 4841 5376 288921063 288921597 0.000000e+00 883
51 TraesCS5B01G503000 chr7A 91.325 415 33 2 2374 2787 79626304 79626716 1.010000e-156 564
52 TraesCS5B01G503000 chr5D 94.656 786 38 1 1591 2372 4661353 4662138 0.000000e+00 1216
53 TraesCS5B01G503000 chr5D 92.472 797 49 5 2780 3576 4662626 4663411 0.000000e+00 1129
54 TraesCS5B01G503000 chr5D 92.271 414 28 3 2374 2785 4662184 4662595 7.760000e-163 584
55 TraesCS5B01G503000 chr6D 89.499 838 79 4 2 837 435847286 435846456 0.000000e+00 1051
56 TraesCS5B01G503000 chr6B 89.286 840 80 5 3 840 133745968 133745137 0.000000e+00 1044
57 TraesCS5B01G503000 chr3B 88.862 835 86 4 1 830 824976227 824975395 0.000000e+00 1020
58 TraesCS5B01G503000 chrUn 88.987 790 84 3 1 789 158032035 158031248 0.000000e+00 974
59 TraesCS5B01G503000 chr5A 97.015 536 12 2 4841 5376 474838446 474837915 0.000000e+00 898
60 TraesCS5B01G503000 chr5A 96.828 536 14 1 4841 5376 331012510 331013042 0.000000e+00 893
61 TraesCS5B01G503000 chr1B 97.015 536 13 1 4841 5376 659232532 659232000 0.000000e+00 898
62 TraesCS5B01G503000 chr4B 96.828 536 11 1 4841 5376 223029904 223030433 0.000000e+00 891
63 TraesCS5B01G503000 chr4B 95.896 536 19 1 4841 5376 655278602 655279134 0.000000e+00 865


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 TraesCS5B01G503000 chr5B 669730121 669735496 5375 False 9928.000000 9928 100.000000 1 5376 1 chr5B.!!$F1 5375
1 TraesCS5B01G503000 chr5B 507221374 507221906 532 True 909.000000 909 97.388000 4841 5376 1 chr5B.!!$R1 535
2 TraesCS5B01G503000 chr7D 52490672 52493088 2416 False 3338.000000 3338 91.786000 1 2398 1 chr7D.!!$F2 2397
3 TraesCS5B01G503000 chr7D 15224985 15226260 1275 False 1616.000000 1616 89.564000 3559 4837 1 chr7D.!!$F1 1278
4 TraesCS5B01G503000 chr2D 16918628 16922285 3657 True 2105.000000 3057 91.549000 3 3576 2 chr2D.!!$R1 3573
5 TraesCS5B01G503000 chr2D 21212299 21213583 1284 False 1628.000000 1628 89.583000 3556 4842 1 chr2D.!!$F1 1286
6 TraesCS5B01G503000 chr1A 38342382 38347227 4845 True 1647.500000 2929 91.949500 3 4841 4 chr1A.!!$R2 4838
7 TraesCS5B01G503000 chr1A 576695854 576696661 807 True 1072.000000 1072 90.820000 1343 2144 1 chr1A.!!$R1 801
8 TraesCS5B01G503000 chr2B 51796228 51802604 6376 True 2362.500000 2767 89.674500 1 4838 2 chr2B.!!$R1 4837
9 TraesCS5B01G503000 chr2B 723976940 723979250 2310 False 1469.000000 1661 90.704500 30 2367 2 chr2B.!!$F1 2337
10 TraesCS5B01G503000 chr6A 193175312 193177359 2047 True 2758.000000 2758 90.931000 2783 4842 1 chr6A.!!$R1 2059
11 TraesCS5B01G503000 chr6A 441293341 441294615 1274 True 1628.000000 1628 89.774000 3559 4832 1 chr6A.!!$R2 1273
12 TraesCS5B01G503000 chr4A 294601268 294602546 1278 False 1748.000000 1748 91.304000 3556 4841 1 chr4A.!!$F1 1285
13 TraesCS5B01G503000 chr4A 605878654 605881917 3263 False 1272.666667 2700 91.098000 1363 4843 3 chr4A.!!$F2 3480
14 TraesCS5B01G503000 chr3A 732951332 732955209 3877 True 1557.000000 1868 92.083000 3 3872 3 chr3A.!!$R3 3869
15 TraesCS5B01G503000 chr3A 297822588 297823372 784 True 1103.000000 1103 91.940000 2783 3576 1 chr3A.!!$R1 793
16 TraesCS5B01G503000 chr3A 101775648 101777707 2059 False 965.333333 1203 92.839667 1591 3576 3 chr3A.!!$F1 1985
17 TraesCS5B01G503000 chr3A 297836841 297837477 636 True 662.000000 662 85.826000 933 1557 1 chr3A.!!$R2 624
18 TraesCS5B01G503000 chr2A 671215379 671219021 3642 False 1418.000000 1845 91.626333 3 3631 3 chr2A.!!$F2 3628
19 TraesCS5B01G503000 chr7B 710046468 710047751 1283 True 1687.000000 1687 90.388000 3557 4842 1 chr7B.!!$R2 1285
20 TraesCS5B01G503000 chr7B 747463023 747464127 1104 False 1341.000000 1341 88.830000 1043 2145 1 chr7B.!!$F2 1102
21 TraesCS5B01G503000 chr7B 710106419 710113765 7346 True 1167.333333 1727 87.761667 15 4840 3 chr7B.!!$R5 4825
22 TraesCS5B01G503000 chr7B 710129124 710133988 4864 True 1155.500000 1729 87.512500 1043 4842 2 chr7B.!!$R6 3799
23 TraesCS5B01G503000 chr7B 610201749 610202281 532 True 893.000000 893 96.828000 4841 5376 1 chr7B.!!$R1 535
24 TraesCS5B01G503000 chr7B 710121757 710122382 625 True 577.000000 577 83.851000 1043 1665 1 chr7B.!!$R4 622
25 TraesCS5B01G503000 chr7B 710080299 710080841 542 True 477.000000 477 83.066000 1043 1586 1 chr7B.!!$R3 543
26 TraesCS5B01G503000 chr7A 128297778 128299272 1494 False 1517.000000 1517 85.152000 3 1529 1 chr7A.!!$F2 1526
27 TraesCS5B01G503000 chr7A 650509897 650510714 817 True 1074.000000 1074 90.568000 1332 2144 1 chr7A.!!$R1 812
28 TraesCS5B01G503000 chr7A 656987808 656988340 532 True 904.000000 904 97.201000 4841 5376 1 chr7A.!!$R2 535
29 TraesCS5B01G503000 chr7A 288921063 288921597 534 False 883.000000 883 96.455000 4841 5376 1 chr7A.!!$F3 535
30 TraesCS5B01G503000 chr5D 4661353 4663411 2058 False 976.333333 1216 93.133000 1591 3576 3 chr5D.!!$F1 1985
31 TraesCS5B01G503000 chr6D 435846456 435847286 830 True 1051.000000 1051 89.499000 2 837 1 chr6D.!!$R1 835
32 TraesCS5B01G503000 chr6B 133745137 133745968 831 True 1044.000000 1044 89.286000 3 840 1 chr6B.!!$R1 837
33 TraesCS5B01G503000 chr3B 824975395 824976227 832 True 1020.000000 1020 88.862000 1 830 1 chr3B.!!$R1 829
34 TraesCS5B01G503000 chrUn 158031248 158032035 787 True 974.000000 974 88.987000 1 789 1 chrUn.!!$R1 788
35 TraesCS5B01G503000 chr5A 474837915 474838446 531 True 898.000000 898 97.015000 4841 5376 1 chr5A.!!$R1 535
36 TraesCS5B01G503000 chr5A 331012510 331013042 532 False 893.000000 893 96.828000 4841 5376 1 chr5A.!!$F1 535
37 TraesCS5B01G503000 chr1B 659232000 659232532 532 True 898.000000 898 97.015000 4841 5376 1 chr1B.!!$R1 535
38 TraesCS5B01G503000 chr4B 223029904 223030433 529 False 891.000000 891 96.828000 4841 5376 1 chr4B.!!$F1 535
39 TraesCS5B01G503000 chr4B 655278602 655279134 532 False 865.000000 865 95.896000 4841 5376 1 chr4B.!!$F2 535

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
970 997 0.420272 AGGCCCTTCCTAACTACCCA 59.580 55.000 0.00 0.00 45.41 4.51 F
1007 1044 0.319083 ACCAAATCACACGGCGTCTA 59.681 50.000 10.85 0.00 0.00 2.59 F
1008 1045 1.066430 ACCAAATCACACGGCGTCTAT 60.066 47.619 10.85 0.22 0.00 1.98 F
1039 1077 1.456705 ATCTGGAGCTCTCGTCCCC 60.457 63.158 14.64 0.00 32.49 4.81 F
2685 5702 0.250234 TGACATGTGGCCAGCTAGAC 59.750 55.000 5.11 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 4280 1.203001 CCCTTGTTAACCTGCCCAAGA 60.203 52.381 2.48 0.00 37.14 3.02 R
2162 4574 1.866015 TGGCACTAGTACAGCTGGAT 58.134 50.000 19.93 5.72 0.00 3.41 R
2515 5530 2.960384 TGGAAGAACAAGACTGTACCGA 59.040 45.455 0.00 0.00 33.45 4.69 R
2965 7607 3.762779 GCATCAAACTGTGAAGCCATAC 58.237 45.455 0.00 0.00 43.66 2.39 R
4630 9312 0.820074 TCGCCACATGTTTTCCCGTT 60.820 50.000 0.00 0.00 0.00 4.44 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
92 97 8.867248 TTTTCGTTAAAACAAAAATGACAAGC 57.133 26.923 0.00 0.00 29.59 4.01
101 106 8.715191 AAACAAAAATGACAAGCTTATGTTGA 57.285 26.923 0.00 0.00 32.57 3.18
105 110 6.403866 AAATGACAAGCTTATGTTGAACCA 57.596 33.333 0.00 0.00 32.57 3.67
221 226 2.814919 ACATAGATCGACCGTCTCATCC 59.185 50.000 0.00 0.00 0.00 3.51
325 331 4.464597 AGTTGTAGTTCAAAACTGGCCAAA 59.535 37.500 7.01 0.00 42.84 3.28
326 332 5.046950 AGTTGTAGTTCAAAACTGGCCAAAA 60.047 36.000 7.01 0.00 42.84 2.44
332 338 5.709631 AGTTCAAAACTGGCCAAAATTTTGT 59.290 32.000 30.07 18.74 41.01 2.83
345 351 6.805760 GCCAAAATTTTGTTGCTTTCTGAAAA 59.194 30.769 25.25 0.00 36.45 2.29
464 471 2.286425 ACCCCTACCAGGCTGCAT 60.286 61.111 9.56 1.43 32.73 3.96
468 475 1.340399 CCCTACCAGGCTGCATCTCA 61.340 60.000 9.56 0.00 32.73 3.27
582 589 1.117749 TCCTCCATCCTCGATGCTGG 61.118 60.000 4.38 4.38 38.59 4.85
586 593 1.072678 CATCCTCGATGCTGGCCAT 59.927 57.895 5.51 0.00 33.17 4.40
593 600 1.141019 GATGCTGGCCATGCAGTTG 59.859 57.895 26.54 8.50 44.04 3.16
602 609 1.518056 CCATGCAGTTGCGTTGTCCT 61.518 55.000 0.00 0.00 45.83 3.85
607 614 1.065551 GCAGTTGCGTTGTCCTTCTTT 59.934 47.619 0.00 0.00 0.00 2.52
617 624 2.043992 TGTCCTTCTTTCCGACCTTCA 58.956 47.619 0.00 0.00 0.00 3.02
729 736 3.713764 ACGATTTCATCAGGAATCTCCCT 59.286 43.478 0.00 0.00 37.19 4.20
775 782 0.800683 CGTGAGACGATTTAGCGGCA 60.801 55.000 1.45 0.00 46.05 5.69
776 783 1.571919 GTGAGACGATTTAGCGGCAT 58.428 50.000 1.45 0.00 43.13 4.40
777 784 2.739292 GTGAGACGATTTAGCGGCATA 58.261 47.619 1.45 0.00 43.13 3.14
778 785 3.318017 GTGAGACGATTTAGCGGCATAT 58.682 45.455 1.45 0.00 43.13 1.78
779 786 4.482386 GTGAGACGATTTAGCGGCATATA 58.518 43.478 1.45 0.00 43.13 0.86
780 787 5.103000 GTGAGACGATTTAGCGGCATATAT 58.897 41.667 1.45 0.00 43.13 0.86
897 921 8.921670 CATAATTTTGGTTTACTGTAGTTTGCC 58.078 33.333 0.00 0.00 0.00 4.52
900 924 2.444010 TGGTTTACTGTAGTTTGCCCCT 59.556 45.455 0.00 0.00 0.00 4.79
914 938 4.974368 TTGCCCCTATATTTTGTGTTCG 57.026 40.909 0.00 0.00 0.00 3.95
953 980 5.527582 AGTGTATTTATCTTGCCGCTAAAGG 59.472 40.000 0.00 0.00 0.00 3.11
969 996 1.592948 AAGGCCCTTCCTAACTACCC 58.407 55.000 0.00 0.00 46.94 3.69
970 997 0.420272 AGGCCCTTCCTAACTACCCA 59.580 55.000 0.00 0.00 45.41 4.51
1007 1044 0.319083 ACCAAATCACACGGCGTCTA 59.681 50.000 10.85 0.00 0.00 2.59
1008 1045 1.066430 ACCAAATCACACGGCGTCTAT 60.066 47.619 10.85 0.22 0.00 1.98
1039 1077 1.456705 ATCTGGAGCTCTCGTCCCC 60.457 63.158 14.64 0.00 32.49 4.81
1040 1078 2.230189 ATCTGGAGCTCTCGTCCCCA 62.230 60.000 14.64 0.20 32.49 4.96
1071 2583 3.028130 GTTCTTTCTCCCGATCTCCTCT 58.972 50.000 0.00 0.00 0.00 3.69
1084 2597 4.824537 CGATCTCCTCTCATCCTAGAACAA 59.175 45.833 0.00 0.00 0.00 2.83
1085 2598 5.476599 CGATCTCCTCTCATCCTAGAACAAT 59.523 44.000 0.00 0.00 0.00 2.71
1095 2608 7.126268 TCTCATCCTAGAACAATCAGAAATCCA 59.874 37.037 0.00 0.00 0.00 3.41
1099 2612 5.884792 CCTAGAACAATCAGAAATCCAAGCT 59.115 40.000 0.00 0.00 0.00 3.74
1167 2684 2.458162 CGAGAAGTCGTCGTCCTCT 58.542 57.895 0.00 0.00 41.57 3.69
1586 3154 2.304470 AGAAGTCTGGCTTTCCTCCTTC 59.696 50.000 0.00 0.00 37.59 3.46
1983 4183 6.602406 AGCTGCACTTAAAATGATGAGAGATT 59.398 34.615 1.02 0.00 0.00 2.40
2105 4306 2.556559 GGGCAGGTTAACAAGGGATTGA 60.557 50.000 8.10 0.00 0.00 2.57
2162 4574 7.232188 TGGATTACCACTATTGTTGGTGTTAA 58.768 34.615 4.23 0.00 41.77 2.01
2201 4613 5.190925 TGCCATAACTACACTATCTGGGTTT 59.809 40.000 0.00 0.00 32.50 3.27
2305 5107 4.586421 TCATACTTCAAAACATGTTGGGCA 59.414 37.500 12.82 0.00 0.00 5.36
2346 5151 1.696884 TGAGGAACATGTGCAGGTGTA 59.303 47.619 6.08 0.00 0.00 2.90
2367 5377 2.027385 GGGCTTGATAAAGCTTGGAGG 58.973 52.381 14.65 0.00 44.86 4.30
2372 5382 5.186198 GCTTGATAAAGCTTGGAGGTTAGA 58.814 41.667 7.63 0.00 42.32 2.10
2515 5530 3.005791 GGTTTGCTGCTTTTGTGGATACT 59.994 43.478 0.00 0.00 37.61 2.12
2525 5540 4.445452 TTTGTGGATACTCGGTACAGTC 57.555 45.455 0.00 0.00 37.61 3.51
2579 5596 7.039270 ACACACAGCAGTAATTTATCGATACA 58.961 34.615 4.16 0.00 0.00 2.29
2584 5601 6.923508 CAGCAGTAATTTATCGATACAGGTGA 59.076 38.462 4.16 0.00 36.97 4.02
2637 5654 0.675633 GCAATGCTCTTTGTGGTGGT 59.324 50.000 0.00 0.00 0.00 4.16
2638 5655 1.336240 GCAATGCTCTTTGTGGTGGTC 60.336 52.381 0.00 0.00 0.00 4.02
2640 5657 2.559668 CAATGCTCTTTGTGGTGGTCAT 59.440 45.455 0.00 0.00 0.00 3.06
2677 5694 4.082571 GGCAATAGATAATGACATGTGGCC 60.083 45.833 1.15 0.00 0.00 5.36
2685 5702 0.250234 TGACATGTGGCCAGCTAGAC 59.750 55.000 5.11 0.00 0.00 2.59
2859 7262 4.464008 AGATGCAGAGGTTGTGAAAAAGA 58.536 39.130 0.00 0.00 0.00 2.52
2965 7607 0.911769 TGGGACAAGATAGCACCTGG 59.088 55.000 0.00 0.00 31.92 4.45
3072 7714 9.624373 ATCATATTTCTTATTGAGTGCTTCTGT 57.376 29.630 0.00 0.00 0.00 3.41
3156 7803 1.699083 TCAATGAGCACTTGTCAGGGA 59.301 47.619 0.00 0.00 0.00 4.20
3167 7814 1.139498 TGTCAGGGATGGGCTTCCAA 61.139 55.000 8.84 0.00 44.86 3.53
3210 7857 8.579850 TTGTTTTATGATTCTATGGTTGAGCT 57.420 30.769 0.00 0.00 0.00 4.09
3215 7862 9.770097 TTTATGATTCTATGGTTGAGCTAGAAG 57.230 33.333 0.00 0.00 35.56 2.85
3299 7947 7.286087 AGCTTCATTTATCAATTACCATGCAGA 59.714 33.333 0.00 0.00 0.00 4.26
3342 7990 0.618981 CCCTTGGTCTACAGGAACCC 59.381 60.000 0.00 0.00 0.00 4.11
3447 8095 6.823689 TCCAAATTAATTGACACTCCTCTAGC 59.176 38.462 0.39 0.00 41.85 3.42
3508 8156 3.273434 CCATGAGGTGTGGTTCTATGTG 58.727 50.000 0.00 0.00 31.96 3.21
3516 8164 0.327924 TGGTTCTATGTGTGCCCAGG 59.672 55.000 0.00 0.00 0.00 4.45
3578 8230 6.548321 ACCACACCTATAATTGTTCTTTCCA 58.452 36.000 0.00 0.00 0.00 3.53
3664 8323 2.025981 AGTGAGCATGTCATTGGCCTTA 60.026 45.455 3.32 0.00 37.56 2.69
3679 8338 7.944554 TCATTGGCCTTAATAATTAGCTAGCTT 59.055 33.333 24.88 7.70 0.00 3.74
3704 8363 3.192001 TCTTCTCTTTCACCATGCATTGC 59.808 43.478 0.00 0.46 0.00 3.56
3769 8430 5.105146 AGCTAGGGACATGAACTTAACTGAG 60.105 44.000 0.00 0.00 0.00 3.35
3841 8502 6.094048 ACATGTACTTGTGCTTATGCTTTAGG 59.906 38.462 13.19 0.00 40.48 2.69
3873 8534 7.942341 ACACTTGTAAAATTGTTCTGATCCCTA 59.058 33.333 0.00 0.00 0.00 3.53
3917 8588 4.579753 AGTATTACTCGAGTTAGTCTGGCC 59.420 45.833 25.44 0.00 0.00 5.36
3920 8591 1.178276 CTCGAGTTAGTCTGGCCACT 58.822 55.000 0.00 0.00 0.00 4.00
4026 8702 7.617225 TGATTTCTTGATTGCAGGATTCAAAT 58.383 30.769 1.52 0.00 29.57 2.32
4038 8714 5.523916 GCAGGATTCAAATAACTAGCTCGAA 59.476 40.000 0.00 0.00 0.00 3.71
4045 8721 7.342769 TCAAATAACTAGCTCGAATGGACTA 57.657 36.000 0.00 0.00 0.00 2.59
4086 8763 6.067217 AGTCTTGGCACTTAATTAGGATGT 57.933 37.500 0.98 0.00 0.00 3.06
4128 8805 7.425577 TTCACTTGATGGATATTTGCTATCG 57.574 36.000 0.00 0.00 37.67 2.92
4240 8921 0.104120 GCCACAACCCACTTTTGGTC 59.896 55.000 0.00 0.00 42.10 4.02
4304 8985 5.527582 AGTTTCTCGCTACAAACATTTCACT 59.472 36.000 0.00 0.00 35.33 3.41
4407 9088 1.083489 TAATGCCACAAGTGTAGCGC 58.917 50.000 0.00 0.00 35.42 5.92
4440 9121 1.268352 TGCCTAATGCCACGAAAACAC 59.732 47.619 0.00 0.00 40.16 3.32
4462 9143 5.971202 CACGGATTGTTGCCATAGTTTATTC 59.029 40.000 0.00 0.00 0.00 1.75
4487 9168 5.401550 CACAATTGACTATTGCCACGAAAT 58.598 37.500 13.59 0.00 46.21 2.17
4493 9174 9.772973 AATTGACTATTGCCACGAAATAGTATA 57.227 29.630 5.22 0.00 46.10 1.47
4530 9211 0.881118 CGTTGGCATAGGTTGTTGCT 59.119 50.000 0.00 0.00 38.88 3.91
4630 9312 1.271488 TGGCATCAGATGAGTGTTGCA 60.271 47.619 15.12 0.00 42.54 4.08
4696 9379 5.010516 AGCACACTTTATTACCACAATTGCA 59.989 36.000 5.05 0.00 0.00 4.08
4767 9450 1.522258 CAAATGCTGTTTCGTGGCAAC 59.478 47.619 0.00 0.00 39.46 4.17
4798 9481 3.386486 TCGCCACAAATCGGTATGTATC 58.614 45.455 0.00 0.00 0.00 2.24
4799 9482 3.127589 CGCCACAAATCGGTATGTATCA 58.872 45.455 0.00 0.00 0.00 2.15
4857 9540 9.298250 TCCTTGTAGTGGCTCTAATATACTAAG 57.702 37.037 0.00 0.00 0.00 2.18
4994 9677 7.775053 TTCCAAAATGACATAGGTTAGCTTT 57.225 32.000 0.00 0.00 0.00 3.51
5316 10012 4.936891 AGTGCTTCTTTTCCATTTGTGTC 58.063 39.130 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 5.682943 AACCAATTTCGTTTTGAGATCGA 57.317 34.783 0.00 0.00 0.00 3.59
12 14 5.116983 CCAAACCAATTTCGTTTTGAGATCG 59.883 40.000 0.00 0.00 31.11 3.69
75 80 9.160496 TCAACATAAGCTTGTCATTTTTGTTTT 57.840 25.926 9.86 0.00 0.00 2.43
92 97 3.120199 CGCCAGAGTTGGTTCAACATAAG 60.120 47.826 12.46 1.45 45.66 1.73
101 106 3.469863 TTCCGCGCCAGAGTTGGTT 62.470 57.895 0.00 0.00 46.80 3.67
105 110 1.668151 GTTCTTCCGCGCCAGAGTT 60.668 57.895 0.00 0.00 0.00 3.01
119 124 1.280457 GACAGTCCATGGAGGGTTCT 58.720 55.000 16.81 5.19 38.24 3.01
221 226 5.467035 AACAAGTACAAATGGAATGGGTG 57.533 39.130 0.00 0.00 0.00 4.61
326 332 9.992910 GAAAATCTTTTCAGAAAGCAACAAAAT 57.007 25.926 9.88 0.00 44.48 1.82
332 338 8.647143 ATTTCGAAAATCTTTTCAGAAAGCAA 57.353 26.923 15.66 12.52 45.15 3.91
345 351 6.640907 GGTTTGCACTACAATTTCGAAAATCT 59.359 34.615 15.66 0.00 38.31 2.40
464 471 2.359169 GGGTCAGGACGGCATGAGA 61.359 63.158 5.51 0.00 35.20 3.27
468 475 3.461773 CTCGGGTCAGGACGGCAT 61.462 66.667 0.00 0.00 0.00 4.40
558 565 1.347050 CATCGAGGATGGAGGAAGCAT 59.653 52.381 0.00 0.00 36.51 3.79
582 589 1.730547 GACAACGCAACTGCATGGC 60.731 57.895 2.12 0.00 42.21 4.40
586 593 0.463654 AGAAGGACAACGCAACTGCA 60.464 50.000 2.12 0.00 42.21 4.41
593 600 0.511653 GTCGGAAAGAAGGACAACGC 59.488 55.000 0.00 0.00 0.00 4.84
602 609 0.034337 CGGGTGAAGGTCGGAAAGAA 59.966 55.000 0.00 0.00 0.00 2.52
645 652 0.106708 GTGGGAAGCTCGCATCCATA 59.893 55.000 14.29 1.19 41.42 2.74
729 736 3.203710 TCACCTTCCCTCCGAACTAGATA 59.796 47.826 0.00 0.00 0.00 1.98
843 867 7.201965 GGTGGGAAAGTAATTCTTTTTGAAGGA 60.202 37.037 4.94 0.00 45.15 3.36
897 921 6.791633 TTTTGGTGCGAACACAAAATATAGGG 60.792 38.462 15.05 0.00 46.60 3.53
953 980 1.065636 GTGTGGGTAGTTAGGAAGGGC 60.066 57.143 0.00 0.00 0.00 5.19
1007 1044 0.321671 CCAGATCCAATCGCCGGTAT 59.678 55.000 1.90 0.00 0.00 2.73
1008 1045 0.757561 TCCAGATCCAATCGCCGGTA 60.758 55.000 1.90 0.00 0.00 4.02
1039 1077 3.565902 GGGAGAAAGAACAACCTGAACTG 59.434 47.826 0.00 0.00 0.00 3.16
1040 1078 3.744530 CGGGAGAAAGAACAACCTGAACT 60.745 47.826 0.00 0.00 0.00 3.01
1071 2583 7.199167 TGGATTTCTGATTGTTCTAGGATGA 57.801 36.000 0.00 0.00 0.00 2.92
1084 2597 3.274288 GGACGAAGCTTGGATTTCTGAT 58.726 45.455 16.00 0.00 0.00 2.90
1085 2598 2.038426 TGGACGAAGCTTGGATTTCTGA 59.962 45.455 16.00 0.00 0.00 3.27
1153 2670 2.937799 GTGAGATAGAGGACGACGACTT 59.062 50.000 0.00 0.00 0.00 3.01
1167 2684 1.783979 GAGAGGGAGGAGGGTGAGATA 59.216 57.143 0.00 0.00 0.00 1.98
1280 2797 2.363795 CAGTAGGACAGGGCGGGA 60.364 66.667 0.00 0.00 0.00 5.14
1288 2835 4.082523 GCAGCGGGCAGTAGGACA 62.083 66.667 0.00 0.00 43.97 4.02
1402 2969 1.026182 GTGATGCAATGGACGAGGCA 61.026 55.000 0.00 0.00 41.00 4.75
1675 3848 8.514594 TCCAACATCTTCACAATAAAATCAGAC 58.485 33.333 0.00 0.00 0.00 3.51
1698 3871 2.118679 ACCCATCGTCTTCATCATCCA 58.881 47.619 0.00 0.00 0.00 3.41
1870 4062 6.600822 GGCAATAGCAGATATCATACCATTGT 59.399 38.462 5.32 0.00 44.61 2.71
1983 4183 8.324306 AGAGGATTCAAGAACAGATTCACATAA 58.676 33.333 0.00 0.00 37.29 1.90
2080 4280 1.203001 CCCTTGTTAACCTGCCCAAGA 60.203 52.381 2.48 0.00 37.14 3.02
2162 4574 1.866015 TGGCACTAGTACAGCTGGAT 58.134 50.000 19.93 5.72 0.00 3.41
2201 4613 3.819368 TCCAGAATTCAACTGAAGTGCA 58.181 40.909 8.44 0.00 37.48 4.57
2305 5107 5.237815 TCACTGAGTATCGCAAAGAAACAT 58.762 37.500 0.00 0.00 38.61 2.71
2311 5114 3.510388 TCCTCACTGAGTATCGCAAAG 57.490 47.619 5.32 0.00 38.61 2.77
2367 5377 4.464597 ACCTCTGAGTGATTCACCTCTAAC 59.535 45.833 13.14 0.23 34.49 2.34
2372 5382 8.228206 TCTATAATACCTCTGAGTGATTCACCT 58.772 37.037 13.14 1.13 34.49 4.00
2471 5481 4.021456 CCATGCATGCATTCCTGTATTCAT 60.021 41.667 30.32 2.79 33.12 2.57
2515 5530 2.960384 TGGAAGAACAAGACTGTACCGA 59.040 45.455 0.00 0.00 33.45 4.69
2550 5565 5.006358 CGATAAATTACTGCTGTGTGTACCC 59.994 44.000 6.48 0.00 0.00 3.69
2579 5596 7.346751 ACAAATCACAAAACTATGTTCACCT 57.653 32.000 0.00 0.00 0.00 4.00
2584 5601 6.723298 TGGGACAAATCACAAAACTATGTT 57.277 33.333 0.00 0.00 34.39 2.71
2637 5654 3.969466 TGCCCATTGAAATCCCTATGA 57.031 42.857 0.00 0.00 0.00 2.15
2638 5655 6.012113 TCTATTGCCCATTGAAATCCCTATG 58.988 40.000 0.00 0.00 0.00 2.23
2640 5657 5.661503 TCTATTGCCCATTGAAATCCCTA 57.338 39.130 0.00 0.00 0.00 3.53
2677 5694 5.407995 GGCTTAATGCTATCAAGTCTAGCTG 59.592 44.000 0.00 0.00 41.73 4.24
2795 7134 7.951347 ATCAATTCTTGCTTCTGTAGGAAAT 57.049 32.000 0.00 0.00 33.45 2.17
2803 7142 4.703575 TCCCTGAATCAATTCTTGCTTCTG 59.296 41.667 4.50 4.87 36.88 3.02
2965 7607 3.762779 GCATCAAACTGTGAAGCCATAC 58.237 45.455 0.00 0.00 43.66 2.39
3072 7714 6.183360 GGTCATGCAATAACTATTGGACGAAA 60.183 38.462 10.65 0.00 44.77 3.46
3156 7803 4.803329 ATACTGAAGATTGGAAGCCCAT 57.197 40.909 0.00 0.00 43.12 4.00
3198 7845 5.482908 ACAACACTTCTAGCTCAACCATAG 58.517 41.667 0.00 0.00 0.00 2.23
3336 7984 3.062466 GCTTTGGAGGCGGGTTCC 61.062 66.667 0.00 0.00 35.20 3.62
3342 7990 2.359107 TCAGCAGCTTTGGAGGCG 60.359 61.111 0.00 0.00 34.52 5.52
3380 8028 7.120579 TGAATGTTACCTTGAACTTATTCGCAT 59.879 33.333 0.00 0.00 37.69 4.73
3447 8095 4.863689 TGCATGTCAAAAGACAAAGTTGTG 59.136 37.500 0.42 0.00 42.43 3.33
3537 8188 2.937519 TGGTAACCACTGTCAATTGCA 58.062 42.857 0.00 1.49 0.00 4.08
3578 8230 5.693104 TCTTAGACGTGCTTTGTCGTAAAAT 59.307 36.000 0.00 0.00 41.24 1.82
3584 8236 2.987149 ACATCTTAGACGTGCTTTGTCG 59.013 45.455 0.00 0.00 41.24 4.35
3619 8271 2.191128 AGTGGACCATGAGTTTCAGC 57.809 50.000 0.00 0.00 0.00 4.26
3679 8338 4.356405 TGCATGGTGAAAGAGAAGAAGA 57.644 40.909 0.00 0.00 0.00 2.87
3704 8363 3.570926 AGTTGTGATTCAATGCAGCAG 57.429 42.857 0.00 0.00 38.38 4.24
3780 8441 6.560253 CACTACTGATTTAAGTTGTGGCTT 57.440 37.500 9.96 0.00 44.79 4.35
3813 8474 4.876107 AGCATAAGCACAAGTACATGTACC 59.124 41.667 28.29 15.02 45.49 3.34
3841 8502 9.243637 TCAGAACAATTTTACAAGTGTAAATGC 57.756 29.630 15.43 2.32 46.19 3.56
3859 8520 5.880332 GCATGTAACTTAGGGATCAGAACAA 59.120 40.000 0.00 0.00 0.00 2.83
3873 8534 4.821805 ACTGTGTAAGCAAGCATGTAACTT 59.178 37.500 0.00 0.00 0.00 2.66
3917 8588 4.749598 GCCCCATTGTTAAAAAGAACAGTG 59.250 41.667 5.17 5.17 43.16 3.66
3920 8591 4.202305 CCAGCCCCATTGTTAAAAAGAACA 60.202 41.667 0.00 0.00 37.54 3.18
4021 8697 6.222038 AGTCCATTCGAGCTAGTTATTTGA 57.778 37.500 0.00 0.00 0.00 2.69
4026 8702 8.101419 TGATCTATAGTCCATTCGAGCTAGTTA 58.899 37.037 0.00 0.00 0.00 2.24
4038 8714 6.672266 AATTGTCCGTGATCTATAGTCCAT 57.328 37.500 0.00 0.00 0.00 3.41
4045 8721 6.986817 CCAAGACTAAATTGTCCGTGATCTAT 59.013 38.462 0.00 0.00 37.66 1.98
4240 8921 1.501741 GTGGTGCTAACATGTGGCG 59.498 57.895 15.96 3.02 0.00 5.69
4462 9143 2.159393 CGTGGCAATAGTCAATTGTGGG 60.159 50.000 5.13 0.00 45.78 4.61
4487 9168 3.485711 CGCTCGTTTCGTGGTGTATACTA 60.486 47.826 4.17 0.00 0.00 1.82
4493 9174 1.947642 GACGCTCGTTTCGTGGTGT 60.948 57.895 0.00 0.00 40.59 4.16
4630 9312 0.820074 TCGCCACATGTTTTCCCGTT 60.820 50.000 0.00 0.00 0.00 4.44
4771 9454 2.006888 ACCGATTTGTGGCGATAAGTG 58.993 47.619 0.00 0.00 0.00 3.16
5173 9866 8.472007 AGAAGAAGAACACTAGAAGAAGAAGA 57.528 34.615 0.00 0.00 0.00 2.87
5174 9867 9.191995 GAAGAAGAAGAACACTAGAAGAAGAAG 57.808 37.037 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.