Multiple sequence alignment - TraesCS2D01G513100

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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 TraesCS2D01G513100 chr2D 100.000 3656 0 0 1 3656 605076496 605080151 0.000000e+00 6752.0
1 TraesCS2D01G513100 chr2D 96.824 850 23 2 2811 3656 617955679 617954830 0.000000e+00 1417.0
2 TraesCS2D01G513100 chr2D 96.667 840 23 3 2818 3653 28060896 28061734 0.000000e+00 1391.0
3 TraesCS2D01G513100 chr2D 89.838 433 40 4 1 432 255642724 255642295 1.480000e-153 553.0
4 TraesCS2D01G513100 chr2D 84.043 282 25 9 429 710 255624786 255624525 1.690000e-63 254.0
5 TraesCS2D01G513100 chr2D 78.906 256 34 14 1222 1465 605180755 605180508 4.890000e-34 156.0
6 TraesCS2D01G513100 chr2A 97.786 1039 22 1 1777 2815 736231538 736230501 0.000000e+00 1790.0
7 TraesCS2D01G513100 chr2A 96.188 892 13 3 711 1602 736233611 736232741 0.000000e+00 1439.0
8 TraesCS2D01G513100 chr2A 89.928 278 18 8 1 275 127013776 127013506 2.090000e-92 350.0
9 TraesCS2D01G513100 chr2A 81.327 407 47 21 1 388 262240684 262240288 1.650000e-78 303.0
10 TraesCS2D01G513100 chr2A 75.360 625 77 39 1 591 52605299 52605880 2.840000e-56 230.0
11 TraesCS2D01G513100 chr2A 86.992 123 15 1 215 337 371682788 371682909 1.770000e-28 137.0
12 TraesCS2D01G513100 chr2A 96.296 81 3 0 1623 1703 736232284 736232204 2.290000e-27 134.0
13 TraesCS2D01G513100 chr3D 97.412 850 17 3 2811 3656 441158823 441159671 0.000000e+00 1443.0
14 TraesCS2D01G513100 chr3D 96.945 851 21 3 2811 3656 19954009 19953159 0.000000e+00 1423.0
15 TraesCS2D01G513100 chr3D 96.824 850 23 2 2811 3656 602248420 602247571 0.000000e+00 1417.0
16 TraesCS2D01G513100 chr3D 96.706 850 23 4 2811 3656 517765243 517766091 0.000000e+00 1410.0
17 TraesCS2D01G513100 chr3D 88.579 394 34 8 1 388 37483228 37483616 5.530000e-128 468.0
18 TraesCS2D01G513100 chr3D 79.398 631 71 21 1 583 2337807 2338426 1.230000e-104 390.0
19 TraesCS2D01G513100 chr3D 86.691 278 25 10 1 275 9652179 9651911 7.680000e-77 298.0
20 TraesCS2D01G513100 chr3D 86.239 109 11 3 431 538 37483694 37483799 8.300000e-22 115.0
21 TraesCS2D01G513100 chr3D 93.182 44 1 1 1462 1503 134949063 134949106 3.050000e-06 63.9
22 TraesCS2D01G513100 chr5D 96.956 854 21 3 2807 3656 297763087 297762235 0.000000e+00 1428.0
23 TraesCS2D01G513100 chr5D 97.262 840 16 3 2824 3656 514934059 514934898 0.000000e+00 1417.0
24 TraesCS2D01G513100 chr5D 88.261 230 19 6 1 226 41230227 41230002 6.020000e-68 268.0
25 TraesCS2D01G513100 chr5D 89.583 48 3 1 1460 1505 510127935 510127982 3.940000e-05 60.2
26 TraesCS2D01G513100 chr1D 96.916 843 22 2 2818 3656 198893664 198892822 0.000000e+00 1410.0
27 TraesCS2D01G513100 chrUn 83.512 746 72 24 1 710 94146299 94145569 0.000000e+00 649.0
28 TraesCS2D01G513100 chrUn 80.482 456 46 29 1 436 3682487 3682055 3.550000e-80 309.0
29 TraesCS2D01G513100 chrUn 92.857 42 3 0 1462 1503 3698186 3698145 1.100000e-05 62.1
30 TraesCS2D01G513100 chr4A 79.912 453 49 27 1 433 730136212 730136642 9.930000e-76 294.0
31 TraesCS2D01G513100 chr1A 75.395 760 95 53 1 714 564251108 564250395 2.150000e-72 283.0
32 TraesCS2D01G513100 chr1A 79.574 235 26 11 488 710 588667029 588667253 8.180000e-32 148.0
33 TraesCS2D01G513100 chr1A 93.333 45 1 1 1462 1504 71070757 71070713 8.470000e-07 65.8
34 TraesCS2D01G513100 chr7A 75.065 774 101 47 1 724 58358205 58357474 3.600000e-70 276.0
35 TraesCS2D01G513100 chr7A 74.834 755 110 40 1 710 201969016 201968297 6.020000e-68 268.0
36 TraesCS2D01G513100 chr7A 92.857 42 3 0 1462 1503 187107690 187107731 1.100000e-05 62.1
37 TraesCS2D01G513100 chr7A 100.000 29 0 0 1501 1529 682007306 682007278 2.000000e-03 54.7
38 TraesCS2D01G513100 chr3B 75.131 764 99 54 1 710 31859503 31860229 1.290000e-69 274.0
39 TraesCS2D01G513100 chr3A 74.769 757 97 42 1 710 737723023 737723732 1.690000e-63 254.0
40 TraesCS2D01G513100 chr3A 92.857 42 3 0 1458 1499 155828403 155828444 1.100000e-05 62.1
41 TraesCS2D01G513100 chr7D 95.349 43 2 0 1462 1504 581299049 581299007 6.550000e-08 69.4
42 TraesCS2D01G513100 chr6A 91.304 46 2 1 1462 1505 21556681 21556726 1.100000e-05 62.1
43 TraesCS2D01G513100 chr7B 100.000 28 0 0 1501 1528 411788274 411788247 7.000000e-03 52.8


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 TraesCS2D01G513100 chr2D 605076496 605080151 3655 False 6752.0 6752 100.000000 1 3656 1 chr2D.!!$F2 3655
1 TraesCS2D01G513100 chr2D 617954830 617955679 849 True 1417.0 1417 96.824000 2811 3656 1 chr2D.!!$R4 845
2 TraesCS2D01G513100 chr2D 28060896 28061734 838 False 1391.0 1391 96.667000 2818 3653 1 chr2D.!!$F1 835
3 TraesCS2D01G513100 chr2A 736230501 736233611 3110 True 1121.0 1790 96.756667 711 2815 3 chr2A.!!$R3 2104
4 TraesCS2D01G513100 chr2A 52605299 52605880 581 False 230.0 230 75.360000 1 591 1 chr2A.!!$F1 590
5 TraesCS2D01G513100 chr3D 441158823 441159671 848 False 1443.0 1443 97.412000 2811 3656 1 chr3D.!!$F3 845
6 TraesCS2D01G513100 chr3D 19953159 19954009 850 True 1423.0 1423 96.945000 2811 3656 1 chr3D.!!$R2 845
7 TraesCS2D01G513100 chr3D 602247571 602248420 849 True 1417.0 1417 96.824000 2811 3656 1 chr3D.!!$R3 845
8 TraesCS2D01G513100 chr3D 517765243 517766091 848 False 1410.0 1410 96.706000 2811 3656 1 chr3D.!!$F4 845
9 TraesCS2D01G513100 chr3D 2337807 2338426 619 False 390.0 390 79.398000 1 583 1 chr3D.!!$F1 582
10 TraesCS2D01G513100 chr3D 37483228 37483799 571 False 291.5 468 87.409000 1 538 2 chr3D.!!$F5 537
11 TraesCS2D01G513100 chr5D 297762235 297763087 852 True 1428.0 1428 96.956000 2807 3656 1 chr5D.!!$R2 849
12 TraesCS2D01G513100 chr5D 514934059 514934898 839 False 1417.0 1417 97.262000 2824 3656 1 chr5D.!!$F2 832
13 TraesCS2D01G513100 chr1D 198892822 198893664 842 True 1410.0 1410 96.916000 2818 3656 1 chr1D.!!$R1 838
14 TraesCS2D01G513100 chrUn 94145569 94146299 730 True 649.0 649 83.512000 1 710 1 chrUn.!!$R3 709
15 TraesCS2D01G513100 chr1A 564250395 564251108 713 True 283.0 283 75.395000 1 714 1 chr1A.!!$R2 713
16 TraesCS2D01G513100 chr7A 58357474 58358205 731 True 276.0 276 75.065000 1 724 1 chr7A.!!$R1 723
17 TraesCS2D01G513100 chr7A 201968297 201969016 719 True 268.0 268 74.834000 1 710 1 chr7A.!!$R2 709
18 TraesCS2D01G513100 chr3B 31859503 31860229 726 False 274.0 274 75.131000 1 710 1 chr3B.!!$F1 709
19 TraesCS2D01G513100 chr3A 737723023 737723732 709 False 254.0 254 74.769000 1 710 1 chr3A.!!$F2 709

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
647 807 0.419865 TCATCCTACCCTTCCCCACA 59.580 55.0 0.0 0.0 0.0 4.17 F
1602 1762 0.175760 AGATGCGCACGTAGGTCAAT 59.824 50.0 14.9 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2317 0.037326 TGTGCTCTACTGAAAGCCGG 60.037 55.0 0.0 0.0 37.60 6.13 R
3501 4710 0.036875 GTTTCAGTCCCCACCTCTGG 59.963 60.0 0.0 0.0 37.29 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.137825 CTCCTCGAGCGTCAGGTTC 59.862 63.158 6.99 0.00 0.00 3.62
413 513 1.710013 GGTGACGTGTGAATCATCGT 58.290 50.000 13.92 13.92 36.85 3.73
414 514 2.066262 GGTGACGTGTGAATCATCGTT 58.934 47.619 14.82 3.12 35.35 3.85
446 571 2.882132 GCCGGCGTTAATGGCTTT 59.118 55.556 12.58 0.00 45.40 3.51
454 582 3.175929 GCGTTAATGGCTTTGCGTAATT 58.824 40.909 0.00 0.00 0.00 1.40
570 708 2.569657 CGTACAGCAGGCCGTACA 59.430 61.111 15.70 0.00 38.29 2.90
591 740 4.899239 GCGCGCCTCACTATGCCT 62.899 66.667 23.24 0.00 0.00 4.75
592 741 2.659897 CGCGCCTCACTATGCCTC 60.660 66.667 0.00 0.00 0.00 4.70
593 742 2.659897 GCGCCTCACTATGCCTCG 60.660 66.667 0.00 0.00 0.00 4.63
594 743 2.659897 CGCCTCACTATGCCTCGC 60.660 66.667 0.00 0.00 0.00 5.03
595 744 2.280457 GCCTCACTATGCCTCGCC 60.280 66.667 0.00 0.00 0.00 5.54
596 745 3.094062 GCCTCACTATGCCTCGCCA 62.094 63.158 0.00 0.00 0.00 5.69
597 746 1.750930 CCTCACTATGCCTCGCCAT 59.249 57.895 0.00 0.00 0.00 4.40
598 747 0.602106 CCTCACTATGCCTCGCCATG 60.602 60.000 0.00 0.00 0.00 3.66
599 748 1.226686 CTCACTATGCCTCGCCATGC 61.227 60.000 0.00 0.00 0.00 4.06
600 749 2.111878 ACTATGCCTCGCCATGCC 59.888 61.111 0.00 0.00 0.00 4.40
601 750 2.111669 CTATGCCTCGCCATGCCA 59.888 61.111 0.00 0.00 0.00 4.92
608 757 3.657448 CTCGCCATGCCACGGTACA 62.657 63.158 0.00 0.00 0.00 2.90
643 803 3.073209 GGATTTCTCATCCTACCCTTCCC 59.927 52.174 0.00 0.00 35.36 3.97
647 807 0.419865 TCATCCTACCCTTCCCCACA 59.580 55.000 0.00 0.00 0.00 4.17
653 813 1.708551 CTACCCTTCCCCACAAAAGGA 59.291 52.381 2.74 0.00 44.02 3.36
669 829 7.446625 CCACAAAAGGATATCTTCTAATCTGGG 59.553 40.741 2.05 0.00 33.94 4.45
670 830 8.213679 CACAAAAGGATATCTTCTAATCTGGGA 58.786 37.037 2.05 0.00 33.94 4.37
677 837 4.451629 TCTTCTAATCTGGGACGTTGAC 57.548 45.455 0.00 0.00 0.00 3.18
703 863 1.067071 CAGGGAGGTTGTACCGAAGAC 60.067 57.143 0.00 0.00 44.90 3.01
755 915 2.009774 CAGGCGAGGTGATAACTTTGG 58.990 52.381 0.00 0.00 0.00 3.28
1054 1214 3.876300 CCGTCGGGCTCTTTCTTG 58.124 61.111 2.34 0.00 0.00 3.02
1105 1265 6.793349 AGATTCTCTGCATCAGTTATTTTGC 58.207 36.000 0.00 0.00 35.67 3.68
1123 1283 2.786777 TGCTACCGTAGACTGTTCTCA 58.213 47.619 9.88 0.00 32.75 3.27
1150 1310 3.691118 CACTTCGACCATCACCATTCATT 59.309 43.478 0.00 0.00 0.00 2.57
1161 1321 3.747010 TCACCATTCATTGTTTTGCATGC 59.253 39.130 11.82 11.82 0.00 4.06
1162 1322 3.498777 CACCATTCATTGTTTTGCATGCA 59.501 39.130 18.46 18.46 0.00 3.96
1187 1347 7.009631 CACGATTGTTTCTCATTACTTCGATCT 59.990 37.037 0.00 0.00 0.00 2.75
1188 1348 7.009631 ACGATTGTTTCTCATTACTTCGATCTG 59.990 37.037 0.00 0.00 0.00 2.90
1189 1349 7.220875 CGATTGTTTCTCATTACTTCGATCTGA 59.779 37.037 0.00 0.00 0.00 3.27
1190 1350 8.954950 ATTGTTTCTCATTACTTCGATCTGAT 57.045 30.769 0.00 0.00 0.00 2.90
1191 1351 7.993821 TGTTTCTCATTACTTCGATCTGATC 57.006 36.000 7.60 7.60 0.00 2.92
1192 1352 7.547227 TGTTTCTCATTACTTCGATCTGATCA 58.453 34.615 17.19 0.00 0.00 2.92
1193 1353 8.200120 TGTTTCTCATTACTTCGATCTGATCAT 58.800 33.333 17.19 0.00 0.00 2.45
1194 1354 8.698854 GTTTCTCATTACTTCGATCTGATCATC 58.301 37.037 17.19 0.00 0.00 2.92
1195 1355 7.516198 TCTCATTACTTCGATCTGATCATCA 57.484 36.000 17.19 0.00 0.00 3.07
1196 1356 7.366513 TCTCATTACTTCGATCTGATCATCAC 58.633 38.462 17.19 0.00 0.00 3.06
1197 1357 6.450545 TCATTACTTCGATCTGATCATCACC 58.549 40.000 17.19 0.00 0.00 4.02
1198 1358 5.852282 TTACTTCGATCTGATCATCACCA 57.148 39.130 17.19 0.00 0.00 4.17
1199 1359 4.952071 ACTTCGATCTGATCATCACCAT 57.048 40.909 17.19 0.00 0.00 3.55
1200 1360 4.880759 ACTTCGATCTGATCATCACCATC 58.119 43.478 17.19 0.00 0.00 3.51
1321 1481 3.564027 GGCAACCTTCCGCGATCG 61.564 66.667 11.69 11.69 0.00 3.69
1402 1562 4.867599 GGATCGGGTCGGCGACAC 62.868 72.222 37.13 34.38 33.68 3.67
1441 1601 1.134818 TCCGACTTCATGGTCCAATCG 60.135 52.381 0.00 0.92 33.07 3.34
1538 1698 7.496263 CGAAGGGAGTATATCTAATCTCGATCA 59.504 40.741 0.00 0.00 27.68 2.92
1600 1760 1.153842 CAGATGCGCACGTAGGTCA 60.154 57.895 14.90 0.00 0.00 4.02
1601 1761 0.735978 CAGATGCGCACGTAGGTCAA 60.736 55.000 14.90 0.00 0.00 3.18
1602 1762 0.175760 AGATGCGCACGTAGGTCAAT 59.824 50.000 14.90 0.00 0.00 2.57
1603 1763 0.577269 GATGCGCACGTAGGTCAATC 59.423 55.000 14.90 0.00 0.00 2.67
1604 1764 0.175760 ATGCGCACGTAGGTCAATCT 59.824 50.000 14.90 0.00 0.00 2.40
1605 1765 0.812549 TGCGCACGTAGGTCAATCTA 59.187 50.000 5.66 0.00 0.00 1.98
1606 1766 1.407618 TGCGCACGTAGGTCAATCTAT 59.592 47.619 5.66 0.00 0.00 1.98
1607 1767 2.052157 GCGCACGTAGGTCAATCTATC 58.948 52.381 0.30 0.00 0.00 2.08
1608 1768 2.307929 CGCACGTAGGTCAATCTATCG 58.692 52.381 0.00 0.00 0.00 2.92
1609 1769 2.662700 GCACGTAGGTCAATCTATCGG 58.337 52.381 0.00 0.00 0.00 4.18
1610 1770 2.607282 GCACGTAGGTCAATCTATCGGG 60.607 54.545 0.00 0.00 0.00 5.14
1611 1771 2.882761 CACGTAGGTCAATCTATCGGGA 59.117 50.000 0.00 0.00 0.00 5.14
1625 1785 9.341899 CAATCTATCGGGAAAAGTTTTAGTTTG 57.658 33.333 0.00 2.67 0.00 2.93
1666 2274 5.991606 CGATCCCAATTTAATCTAGCTGTCA 59.008 40.000 0.00 0.00 0.00 3.58
1678 2286 0.181114 AGCTGTCACTTGTCCTTGCA 59.819 50.000 0.00 0.00 0.00 4.08
1708 2316 3.015753 GGTCTTCCCCAGTCCCCC 61.016 72.222 0.00 0.00 0.00 5.40
1723 2331 3.721868 CCCCCGGCTTTCAGTAGA 58.278 61.111 0.00 0.00 0.00 2.59
1724 2332 1.522569 CCCCCGGCTTTCAGTAGAG 59.477 63.158 0.00 0.00 0.00 2.43
1725 2333 1.153349 CCCCGGCTTTCAGTAGAGC 60.153 63.158 0.00 0.00 38.17 4.09
1726 2334 1.596934 CCCGGCTTTCAGTAGAGCA 59.403 57.895 0.00 0.00 40.63 4.26
1727 2335 0.741221 CCCGGCTTTCAGTAGAGCAC 60.741 60.000 0.00 0.00 40.63 4.40
1728 2336 0.037326 CCGGCTTTCAGTAGAGCACA 60.037 55.000 0.00 0.00 40.63 4.57
1729 2337 1.608025 CCGGCTTTCAGTAGAGCACAA 60.608 52.381 0.00 0.00 40.63 3.33
1730 2338 2.143122 CGGCTTTCAGTAGAGCACAAA 58.857 47.619 0.00 0.00 40.63 2.83
1731 2339 2.548057 CGGCTTTCAGTAGAGCACAAAA 59.452 45.455 0.00 0.00 40.63 2.44
1732 2340 3.003275 CGGCTTTCAGTAGAGCACAAAAA 59.997 43.478 0.00 0.00 40.63 1.94
1733 2341 4.290969 GGCTTTCAGTAGAGCACAAAAAC 58.709 43.478 0.00 0.00 40.63 2.43
1734 2342 3.968724 GCTTTCAGTAGAGCACAAAAACG 59.031 43.478 0.00 0.00 38.73 3.60
1735 2343 3.602390 TTCAGTAGAGCACAAAAACGC 57.398 42.857 0.00 0.00 0.00 4.84
1736 2344 2.833794 TCAGTAGAGCACAAAAACGCT 58.166 42.857 0.00 0.00 42.42 5.07
1737 2345 3.985008 TCAGTAGAGCACAAAAACGCTA 58.015 40.909 0.00 0.00 38.99 4.26
1738 2346 4.566004 TCAGTAGAGCACAAAAACGCTAT 58.434 39.130 0.00 0.00 38.99 2.97
1739 2347 4.994852 TCAGTAGAGCACAAAAACGCTATT 59.005 37.500 0.00 0.00 38.99 1.73
1740 2348 5.082059 CAGTAGAGCACAAAAACGCTATTG 58.918 41.667 0.00 0.00 38.99 1.90
1741 2349 2.933769 AGAGCACAAAAACGCTATTGC 58.066 42.857 0.00 0.00 38.99 3.56
1742 2350 1.985684 GAGCACAAAAACGCTATTGCC 59.014 47.619 0.00 0.00 38.99 4.52
1743 2351 1.339610 AGCACAAAAACGCTATTGCCA 59.660 42.857 0.00 0.00 36.50 4.92
1744 2352 1.455408 GCACAAAAACGCTATTGCCAC 59.545 47.619 0.00 0.00 35.36 5.01
1745 2353 2.058057 CACAAAAACGCTATTGCCACC 58.942 47.619 0.00 0.00 35.36 4.61
1746 2354 1.000394 ACAAAAACGCTATTGCCACCC 60.000 47.619 0.00 0.00 35.36 4.61
1747 2355 1.000283 CAAAAACGCTATTGCCACCCA 60.000 47.619 0.00 0.00 35.36 4.51
1748 2356 1.333177 AAAACGCTATTGCCACCCAA 58.667 45.000 0.00 0.00 37.94 4.12
1749 2357 0.601057 AAACGCTATTGCCACCCAAC 59.399 50.000 0.00 0.00 35.99 3.77
1750 2358 1.248101 AACGCTATTGCCACCCAACC 61.248 55.000 0.00 0.00 35.99 3.77
1751 2359 2.760159 CGCTATTGCCACCCAACCG 61.760 63.158 0.00 0.00 35.99 4.44
1752 2360 2.414785 GCTATTGCCACCCAACCGG 61.415 63.158 0.00 0.00 35.99 5.28
1758 2366 4.939368 CCACCCAACCGGCGTGAA 62.939 66.667 6.01 0.00 36.23 3.18
1759 2367 3.656045 CACCCAACCGGCGTGAAC 61.656 66.667 6.01 0.00 36.23 3.18
1760 2368 3.868985 ACCCAACCGGCGTGAACT 61.869 61.111 6.01 0.00 33.26 3.01
1761 2369 2.593436 CCCAACCGGCGTGAACTT 60.593 61.111 6.01 0.00 0.00 2.66
1762 2370 2.190841 CCCAACCGGCGTGAACTTT 61.191 57.895 6.01 0.00 0.00 2.66
1763 2371 1.008995 CCAACCGGCGTGAACTTTG 60.009 57.895 6.01 0.00 0.00 2.77
1764 2372 1.657181 CAACCGGCGTGAACTTTGC 60.657 57.895 6.01 0.00 0.00 3.68
1765 2373 2.841160 AACCGGCGTGAACTTTGCC 61.841 57.895 6.01 0.00 45.39 4.52
1766 2374 2.978010 CCGGCGTGAACTTTGCCT 60.978 61.111 6.01 0.00 46.67 4.75
1767 2375 2.551912 CCGGCGTGAACTTTGCCTT 61.552 57.895 6.01 0.00 46.67 4.35
1768 2376 1.358759 CGGCGTGAACTTTGCCTTT 59.641 52.632 0.00 0.00 46.67 3.11
1769 2377 0.934436 CGGCGTGAACTTTGCCTTTG 60.934 55.000 0.00 0.00 46.67 2.77
1770 2378 0.597377 GGCGTGAACTTTGCCTTTGG 60.597 55.000 0.00 0.00 45.40 3.28
1771 2379 0.102300 GCGTGAACTTTGCCTTTGGT 59.898 50.000 0.00 0.00 0.00 3.67
1772 2380 1.864029 GCGTGAACTTTGCCTTTGGTC 60.864 52.381 0.00 0.00 0.00 4.02
1773 2381 1.596954 CGTGAACTTTGCCTTTGGTCG 60.597 52.381 0.00 0.00 0.00 4.79
1774 2382 0.383949 TGAACTTTGCCTTTGGTCGC 59.616 50.000 0.00 0.00 0.00 5.19
1775 2383 0.660300 GAACTTTGCCTTTGGTCGCG 60.660 55.000 0.00 0.00 0.00 5.87
1967 3167 3.430042 ACGTGAGTACCAAGTAGGAGA 57.570 47.619 0.00 0.00 46.88 3.71
2027 3227 8.319143 TGTCTATAGCTTACCAAGTTTTTGTC 57.681 34.615 0.00 0.00 32.21 3.18
2045 3245 1.834263 GTCTAGCTGACCCCTGTGATT 59.166 52.381 0.00 0.00 39.69 2.57
2115 3315 0.620556 TGGGGTGAAGAGGATTCTGC 59.379 55.000 0.00 0.00 32.79 4.26
2198 3398 3.623060 AGTGCGATTACATAGGCAACAAG 59.377 43.478 0.00 0.00 37.12 3.16
2285 3485 0.527565 ATCTGAACACCGCATTTGGC 59.472 50.000 0.00 0.00 39.90 4.52
2325 3525 2.030893 ACGTCCATTTTGTGTGAGCATG 60.031 45.455 0.00 0.00 0.00 4.06
2384 3584 7.509141 TGATCAGATTGTTTGCTCTGTTTTA 57.491 32.000 0.00 0.00 39.87 1.52
2502 3702 3.963428 AGAGCTAACAACTACTGTGGG 57.037 47.619 0.00 0.00 38.67 4.61
2708 3908 0.745845 CGATATGCATAGGCTGGGGC 60.746 60.000 12.79 0.00 41.91 5.80
2747 3947 7.832685 GGGAAGTTAAACCCAACAGTAGATTAT 59.167 37.037 0.00 0.00 44.96 1.28
2865 4065 5.713025 CCAAAGGCCAATACATATACATGC 58.287 41.667 5.01 0.00 35.39 4.06
2875 4075 7.360861 CCAATACATATACATGCGTGGTAAAGG 60.361 40.741 11.36 5.24 35.39 3.11
2935 4136 6.963083 AGAGACTATACACATCTAACACCC 57.037 41.667 0.00 0.00 0.00 4.61
3066 4270 3.065510 GCACATAGTGAAGAGCGAGAGTA 59.934 47.826 0.58 0.00 35.23 2.59
3159 4365 1.202417 ACGCGCAATACTGATAGCACT 60.202 47.619 5.73 0.00 0.00 4.40
3160 4366 1.190984 CGCGCAATACTGATAGCACTG 59.809 52.381 8.75 0.00 0.00 3.66
3294 4503 3.593096 TCTGTACTCGAGCGAGAAACTA 58.407 45.455 24.81 12.03 44.53 2.24
3444 4653 0.771755 AGAGCGGGGAAAGAAAAGGT 59.228 50.000 0.00 0.00 0.00 3.50
3501 4710 1.964933 GGAGGAGGTGACTATAGTGGC 59.035 57.143 10.90 2.44 44.43 5.01
3513 4722 2.194951 ATAGTGGCCAGAGGTGGGGA 62.195 60.000 5.11 0.00 45.17 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.076339 CCTTCCTCTCCCTCTCGCT 60.076 63.158 0.00 0.00 0.00 4.93
264 319 1.670590 AGCTTCTGCGCTCTTGACT 59.329 52.632 9.73 0.00 45.42 3.41
387 487 2.048222 CACACGTCACCGCCTGAT 60.048 61.111 0.00 0.00 37.70 2.90
398 498 0.796312 GGCAACGATGATTCACACGT 59.204 50.000 12.71 12.71 37.65 4.49
454 582 1.202557 ACCCTAATTAATTCGGCGCGA 60.203 47.619 12.10 0.00 0.00 5.87
469 597 2.185867 CAGCCGCGCTAAACCCTA 59.814 61.111 5.56 0.00 36.40 3.53
495 632 1.375780 GGGCCCACGCGTACTTAAA 60.376 57.895 19.95 0.00 35.02 1.52
574 712 4.899239 AGGCATAGTGAGGCGCGC 62.899 66.667 25.94 25.94 36.55 6.86
591 740 3.696676 TGTACCGTGGCATGGCGA 61.697 61.111 25.52 11.22 0.00 5.54
592 741 3.496131 GTGTACCGTGGCATGGCG 61.496 66.667 25.52 7.37 0.00 5.69
593 742 3.131478 GGTGTACCGTGGCATGGC 61.131 66.667 25.52 13.29 0.00 4.40
628 778 0.419865 TGTGGGGAAGGGTAGGATGA 59.580 55.000 0.00 0.00 0.00 2.92
643 803 7.446625 CCCAGATTAGAAGATATCCTTTTGTGG 59.553 40.741 0.00 0.00 34.68 4.17
647 807 7.071321 ACGTCCCAGATTAGAAGATATCCTTTT 59.929 37.037 0.00 0.00 34.68 2.27
653 813 6.515200 CGTCAACGTCCCAGATTAGAAGATAT 60.515 42.308 0.00 0.00 34.11 1.63
677 837 0.949105 GTACAACCTCCCTGCACACG 60.949 60.000 0.00 0.00 0.00 4.49
682 842 0.391263 CTTCGGTACAACCTCCCTGC 60.391 60.000 0.00 0.00 35.66 4.85
703 863 1.411246 TCCCATATCCCGTTCACTTCG 59.589 52.381 0.00 0.00 0.00 3.79
755 915 6.262273 TCAAAGTTCAAGTAGGAATCACCAAC 59.738 38.462 0.00 0.00 42.04 3.77
942 1102 0.458716 GCTCTCTAAGTGACGGTGGC 60.459 60.000 0.00 0.00 0.00 5.01
1050 1210 1.005748 CGCACCACTGAGAGCAAGA 60.006 57.895 0.00 0.00 0.00 3.02
1051 1211 1.287730 GACGCACCACTGAGAGCAAG 61.288 60.000 0.00 0.00 0.00 4.01
1052 1212 1.300931 GACGCACCACTGAGAGCAA 60.301 57.895 0.00 0.00 0.00 3.91
1053 1213 2.147315 GAGACGCACCACTGAGAGCA 62.147 60.000 0.00 0.00 0.00 4.26
1054 1214 1.445238 GAGACGCACCACTGAGAGC 60.445 63.158 0.00 0.00 0.00 4.09
1105 1265 5.297029 TGATGATGAGAACAGTCTACGGTAG 59.703 44.000 8.91 8.91 32.80 3.18
1123 1283 2.501316 TGGTGATGGTCGAAGTGATGAT 59.499 45.455 0.00 0.00 0.00 2.45
1150 1310 2.505628 ACAATCGTGCATGCAAAACA 57.494 40.000 24.58 6.78 0.00 2.83
1161 1321 6.389622 TCGAAGTAATGAGAAACAATCGTG 57.610 37.500 0.00 0.00 0.00 4.35
1162 1322 7.009631 CAGATCGAAGTAATGAGAAACAATCGT 59.990 37.037 0.00 0.00 0.00 3.73
1187 1347 6.516028 GCATGCAAATTAGATGGTGATGATCA 60.516 38.462 14.21 0.00 0.00 2.92
1188 1348 5.862323 GCATGCAAATTAGATGGTGATGATC 59.138 40.000 14.21 0.00 0.00 2.92
1189 1349 5.303333 TGCATGCAAATTAGATGGTGATGAT 59.697 36.000 20.30 0.00 0.00 2.45
1190 1350 4.645588 TGCATGCAAATTAGATGGTGATGA 59.354 37.500 20.30 0.00 0.00 2.92
1191 1351 4.743151 GTGCATGCAAATTAGATGGTGATG 59.257 41.667 24.58 0.00 0.00 3.07
1192 1352 4.498513 CGTGCATGCAAATTAGATGGTGAT 60.499 41.667 24.58 0.00 0.00 3.06
1193 1353 3.181498 CGTGCATGCAAATTAGATGGTGA 60.181 43.478 24.58 0.00 0.00 4.02
1194 1354 3.110358 CGTGCATGCAAATTAGATGGTG 58.890 45.455 24.58 0.00 0.00 4.17
1195 1355 3.016031 TCGTGCATGCAAATTAGATGGT 58.984 40.909 24.58 0.00 0.00 3.55
1196 1356 3.696281 TCGTGCATGCAAATTAGATGG 57.304 42.857 24.58 3.51 0.00 3.51
1197 1357 4.665212 AGTTCGTGCATGCAAATTAGATG 58.335 39.130 24.58 3.11 0.00 2.90
1198 1358 4.970662 AGTTCGTGCATGCAAATTAGAT 57.029 36.364 24.58 2.45 0.00 1.98
1199 1359 6.292865 GCTATAGTTCGTGCATGCAAATTAGA 60.293 38.462 24.58 13.78 0.00 2.10
1200 1360 5.848036 GCTATAGTTCGTGCATGCAAATTAG 59.152 40.000 24.58 16.05 0.00 1.73
1321 1481 2.183046 GACTCAGCTGCGAGGTCC 59.817 66.667 11.40 9.31 37.34 4.46
1402 1562 3.969642 GAAGCGGCCGGTTGCATTG 62.970 63.158 43.84 5.61 43.89 2.82
1551 1711 8.366401 TGATATGCCATCACTTTTCAAGAAAAA 58.634 29.630 9.05 0.00 39.49 1.94
1554 1714 6.855836 GTGATATGCCATCACTTTTCAAGAA 58.144 36.000 17.13 0.00 43.62 2.52
1555 1715 6.441093 GTGATATGCCATCACTTTTCAAGA 57.559 37.500 17.13 0.00 43.62 3.02
1600 1760 9.074576 ACAAACTAAAACTTTTCCCGATAGATT 57.925 29.630 0.00 0.00 39.76 2.40
1601 1761 8.631480 ACAAACTAAAACTTTTCCCGATAGAT 57.369 30.769 0.00 0.00 39.76 1.98
1602 1762 8.992073 GTACAAACTAAAACTTTTCCCGATAGA 58.008 33.333 0.00 0.00 39.76 1.98
1603 1763 8.776470 TGTACAAACTAAAACTTTTCCCGATAG 58.224 33.333 0.00 0.00 0.00 2.08
1604 1764 8.674263 TGTACAAACTAAAACTTTTCCCGATA 57.326 30.769 0.00 0.00 0.00 2.92
1605 1765 7.571080 TGTACAAACTAAAACTTTTCCCGAT 57.429 32.000 0.00 0.00 0.00 4.18
1606 1766 6.998968 TGTACAAACTAAAACTTTTCCCGA 57.001 33.333 0.00 0.00 0.00 5.14
1607 1767 7.112426 CGAATGTACAAACTAAAACTTTTCCCG 59.888 37.037 0.00 0.00 0.00 5.14
1608 1768 7.916977 ACGAATGTACAAACTAAAACTTTTCCC 59.083 33.333 0.00 0.00 0.00 3.97
1609 1769 8.739461 CACGAATGTACAAACTAAAACTTTTCC 58.261 33.333 0.00 0.00 0.00 3.13
1610 1770 9.493206 TCACGAATGTACAAACTAAAACTTTTC 57.507 29.630 0.00 0.00 0.00 2.29
1625 1785 3.421231 GGATCGACGAATCACGAATGTAC 59.579 47.826 0.00 0.00 45.77 2.90
1666 2274 0.106708 TCTTCGCTGCAAGGACAAGT 59.893 50.000 0.00 0.00 0.00 3.16
1678 2286 2.100605 GAAGACCCAACATCTTCGCT 57.899 50.000 0.00 0.00 41.90 4.93
1706 2314 1.522569 CTCTACTGAAAGCCGGGGG 59.477 63.158 2.18 0.00 37.60 5.40
1707 2315 1.153349 GCTCTACTGAAAGCCGGGG 60.153 63.158 2.18 0.00 37.60 5.73
1708 2316 0.741221 GTGCTCTACTGAAAGCCGGG 60.741 60.000 2.18 0.00 37.60 5.73
1709 2317 0.037326 TGTGCTCTACTGAAAGCCGG 60.037 55.000 0.00 0.00 37.60 6.13
1710 2318 1.795768 TTGTGCTCTACTGAAAGCCG 58.204 50.000 0.00 0.00 37.60 5.52
1711 2319 4.290969 GTTTTTGTGCTCTACTGAAAGCC 58.709 43.478 0.00 0.00 37.60 4.35
1712 2320 3.968724 CGTTTTTGTGCTCTACTGAAAGC 59.031 43.478 0.00 0.00 37.60 3.51
1713 2321 3.968724 GCGTTTTTGTGCTCTACTGAAAG 59.031 43.478 0.00 0.00 42.29 2.62
1714 2322 3.625764 AGCGTTTTTGTGCTCTACTGAAA 59.374 39.130 0.00 0.00 36.53 2.69
1715 2323 3.202906 AGCGTTTTTGTGCTCTACTGAA 58.797 40.909 0.00 0.00 36.53 3.02
1716 2324 2.833794 AGCGTTTTTGTGCTCTACTGA 58.166 42.857 0.00 0.00 36.53 3.41
1717 2325 4.928661 ATAGCGTTTTTGTGCTCTACTG 57.071 40.909 0.00 0.00 42.48 2.74
1718 2326 4.378459 GCAATAGCGTTTTTGTGCTCTACT 60.378 41.667 4.57 0.00 42.48 2.57
1719 2327 3.846335 GCAATAGCGTTTTTGTGCTCTAC 59.154 43.478 4.57 0.00 42.48 2.59
1720 2328 3.119990 GGCAATAGCGTTTTTGTGCTCTA 60.120 43.478 4.57 0.00 42.48 2.43
1721 2329 2.351738 GGCAATAGCGTTTTTGTGCTCT 60.352 45.455 4.57 0.00 42.48 4.09
1722 2330 1.985684 GGCAATAGCGTTTTTGTGCTC 59.014 47.619 4.57 0.00 42.48 4.26
1723 2331 1.339610 TGGCAATAGCGTTTTTGTGCT 59.660 42.857 4.57 0.00 45.04 4.40
1724 2332 1.455408 GTGGCAATAGCGTTTTTGTGC 59.545 47.619 4.57 0.00 43.41 4.57
1725 2333 2.058057 GGTGGCAATAGCGTTTTTGTG 58.942 47.619 4.57 0.00 43.41 3.33
1726 2334 1.000394 GGGTGGCAATAGCGTTTTTGT 60.000 47.619 4.57 0.00 43.41 2.83
1727 2335 1.000283 TGGGTGGCAATAGCGTTTTTG 60.000 47.619 0.00 0.00 43.41 2.44
1728 2336 1.333177 TGGGTGGCAATAGCGTTTTT 58.667 45.000 0.00 0.00 43.41 1.94
1729 2337 1.000394 GTTGGGTGGCAATAGCGTTTT 60.000 47.619 0.00 0.00 43.41 2.43
1730 2338 0.601057 GTTGGGTGGCAATAGCGTTT 59.399 50.000 0.00 0.00 43.41 3.60
1731 2339 1.248101 GGTTGGGTGGCAATAGCGTT 61.248 55.000 0.00 0.00 43.41 4.84
1732 2340 1.677633 GGTTGGGTGGCAATAGCGT 60.678 57.895 0.00 0.00 43.41 5.07
1733 2341 2.760159 CGGTTGGGTGGCAATAGCG 61.760 63.158 0.00 0.00 43.41 4.26
1734 2342 2.414785 CCGGTTGGGTGGCAATAGC 61.415 63.158 0.00 0.00 41.10 2.97
1735 2343 3.918544 CCGGTTGGGTGGCAATAG 58.081 61.111 0.00 0.00 0.00 1.73
1743 2351 2.897172 AAAGTTCACGCCGGTTGGGT 62.897 55.000 1.90 0.00 41.52 4.51
1744 2352 2.190841 AAAGTTCACGCCGGTTGGG 61.191 57.895 1.90 0.00 39.58 4.12
1745 2353 1.008995 CAAAGTTCACGCCGGTTGG 60.009 57.895 1.90 0.00 38.77 3.77
1746 2354 1.657181 GCAAAGTTCACGCCGGTTG 60.657 57.895 1.90 0.16 0.00 3.77
1747 2355 2.719354 GCAAAGTTCACGCCGGTT 59.281 55.556 1.90 0.00 0.00 4.44
1748 2356 3.284449 GGCAAAGTTCACGCCGGT 61.284 61.111 1.90 0.00 35.79 5.28
1751 2359 0.597377 CCAAAGGCAAAGTTCACGCC 60.597 55.000 3.32 3.32 46.62 5.68
1752 2360 0.102300 ACCAAAGGCAAAGTTCACGC 59.898 50.000 0.00 0.00 0.00 5.34
1753 2361 1.596954 CGACCAAAGGCAAAGTTCACG 60.597 52.381 0.00 0.00 0.00 4.35
1754 2362 1.864029 GCGACCAAAGGCAAAGTTCAC 60.864 52.381 0.00 0.00 0.00 3.18
1755 2363 0.383949 GCGACCAAAGGCAAAGTTCA 59.616 50.000 0.00 0.00 0.00 3.18
1756 2364 0.660300 CGCGACCAAAGGCAAAGTTC 60.660 55.000 0.00 0.00 0.00 3.01
1757 2365 1.358759 CGCGACCAAAGGCAAAGTT 59.641 52.632 0.00 0.00 0.00 2.66
1758 2366 3.030652 CGCGACCAAAGGCAAAGT 58.969 55.556 0.00 0.00 0.00 2.66
1759 2367 2.429069 GCGCGACCAAAGGCAAAG 60.429 61.111 12.10 0.00 0.00 2.77
1760 2368 3.972276 GGCGCGACCAAAGGCAAA 61.972 61.111 12.10 0.00 38.86 3.68
2027 3227 1.833630 TCAATCACAGGGGTCAGCTAG 59.166 52.381 0.00 0.00 0.00 3.42
2045 3245 2.451493 TGGTTCCCCAAGCCCTCA 60.451 61.111 0.00 0.00 37.98 3.86
2099 3299 3.006247 GTTCAGCAGAATCCTCTTCACC 58.994 50.000 0.00 0.00 35.92 4.02
2115 3315 4.261801 CCAATAGGGTGTAGGTTGTTCAG 58.738 47.826 0.00 0.00 0.00 3.02
2285 3485 3.689161 ACGTACCATGGTCAATGATGTTG 59.311 43.478 23.76 2.69 38.72 3.33
2314 3514 5.088680 TCTCATCATAACATGCTCACACA 57.911 39.130 0.00 0.00 0.00 3.72
2325 3525 8.896744 TGTTGATCCAATCTTTCTCATCATAAC 58.103 33.333 0.00 0.00 0.00 1.89
2384 3584 9.686683 AATAAGTCATATAGAGCAACAAAAGGT 57.313 29.630 0.00 0.00 0.00 3.50
2502 3702 1.440145 GATAGTTCTTGGCCTGCCGC 61.440 60.000 3.32 0.00 39.42 6.53
2515 3715 1.767088 GGAGTAAAGGGGCGGATAGTT 59.233 52.381 0.00 0.00 0.00 2.24
2605 3805 2.502142 TGTTCCAGCTGCTTCATGAT 57.498 45.000 8.66 0.00 0.00 2.45
2676 3876 6.965500 CCTATGCATATCGCTTCATCATTTTC 59.035 38.462 6.92 0.00 43.06 2.29
2708 3908 7.371159 GGTTTAACTTCCCAATTTTGAGAGAG 58.629 38.462 0.00 0.00 0.00 3.20
2747 3947 5.227569 ACAGAATACAGACCATGTCACAA 57.772 39.130 0.00 0.00 42.70 3.33
2865 4065 0.879090 GTTTCCTGCCCTTTACCACG 59.121 55.000 0.00 0.00 0.00 4.94
2935 4136 0.323725 CCACCATGAGTTTGAGGGGG 60.324 60.000 0.00 0.00 38.58 5.40
3294 4503 4.843728 TGGAAGACAAAGAAACAGACTGT 58.156 39.130 1.07 1.07 0.00 3.55
3444 4653 1.216444 GTGGCACGATCTCTCAGCA 59.784 57.895 0.00 0.00 0.00 4.41
3501 4710 0.036875 GTTTCAGTCCCCACCTCTGG 59.963 60.000 0.00 0.00 37.29 3.86
3513 4722 4.487714 TCCTGAGTCAGTTTGTTTCAGT 57.512 40.909 18.74 0.00 34.81 3.41


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

AutoCloner maintained by Alex Coulton.