Multiple sequence alignment - TraesCS4A01G368300

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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 TraesCS4A01G368300 chr4A 100.000 4283 0 0 1784 6066 641294118 641289836 0.000000e+00 7910.0
1 TraesCS4A01G368300 chr4A 100.000 1445 0 0 1 1445 641295901 641294457 0.000000e+00 2669.0
2 TraesCS4A01G368300 chr4A 100.000 944 0 0 5123 6066 600963704 600964647 0.000000e+00 1744.0
3 TraesCS4A01G368300 chr4A 77.143 420 74 17 199 606 116327570 116327979 2.200000e-54 224.0
4 TraesCS4A01G368300 chr5D 93.878 2532 92 24 2576 5091 531291387 531293871 0.000000e+00 3759.0
5 TraesCS4A01G368300 chr5D 76.309 1815 382 39 2784 4580 40978621 40980405 0.000000e+00 926.0
6 TraesCS4A01G368300 chr5D 92.202 654 39 4 610 1263 531287731 531288372 0.000000e+00 915.0
7 TraesCS4A01G368300 chr5D 85.358 601 57 19 1784 2362 531289682 531290273 1.460000e-165 593.0
8 TraesCS4A01G368300 chr5B 100.000 944 0 0 5123 6066 6600759 6599816 0.000000e+00 1744.0
9 TraesCS4A01G368300 chr5B 99.368 950 4 1 5119 6066 480429557 480430506 0.000000e+00 1720.0
10 TraesCS4A01G368300 chr5B 76.620 1805 376 36 2784 4571 35156097 35157872 0.000000e+00 953.0
11 TraesCS4A01G368300 chr5B 76.680 1801 353 56 2784 4555 35146892 35148654 0.000000e+00 937.0
12 TraesCS4A01G368300 chr5B 89.481 732 55 11 623 1351 670382939 670383651 0.000000e+00 905.0
13 TraesCS4A01G368300 chr5B 89.052 749 54 13 610 1351 670437637 670438364 0.000000e+00 904.0
14 TraesCS4A01G368300 chr5B 86.818 660 34 14 4474 5124 670476483 670477098 0.000000e+00 688.0
15 TraesCS4A01G368300 chr5B 79.541 567 68 25 1833 2362 670446476 670447031 1.610000e-95 361.0
16 TraesCS4A01G368300 chr5B 83.439 314 37 9 1046 1349 670466668 670466976 1.670000e-70 278.0
17 TraesCS4A01G368300 chr5B 98.333 60 1 0 4422 4481 670471022 670471081 8.320000e-19 106.0
18 TraesCS4A01G368300 chr5B 87.324 71 5 1 646 716 670466602 670466668 1.810000e-10 78.7
19 TraesCS4A01G368300 chr4B 99.894 943 1 0 5124 6066 37539056 37538114 0.000000e+00 1736.0
20 TraesCS4A01G368300 chr4B 87.004 277 27 8 75 343 203204141 203203866 2.750000e-78 303.0
21 TraesCS4A01G368300 chr4B 88.095 84 10 0 4048 4131 628495098 628495181 3.870000e-17 100.0
22 TraesCS4A01G368300 chr6B 99.788 943 2 0 5124 6066 129766107 129767049 0.000000e+00 1731.0
23 TraesCS4A01G368300 chr2B 99.474 950 4 1 5117 6066 62979340 62980288 0.000000e+00 1725.0
24 TraesCS4A01G368300 chr2B 99.130 575 5 0 1 575 587240291 587240865 0.000000e+00 1035.0
25 TraesCS4A01G368300 chr2B 75.272 368 77 14 2873 3233 747237711 747238071 4.860000e-36 163.0
26 TraesCS4A01G368300 chr2B 84.722 72 11 0 4485 4556 747239394 747239465 8.430000e-09 73.1
27 TraesCS4A01G368300 chr1B 99.576 943 4 0 5124 6066 15631160 15632102 0.000000e+00 1720.0
28 TraesCS4A01G368300 chr1B 99.470 943 5 0 5124 6066 431458936 431459878 0.000000e+00 1714.0
29 TraesCS4A01G368300 chr1B 98.689 610 7 1 1 610 16461583 16462191 0.000000e+00 1081.0
30 TraesCS4A01G368300 chr1B 84.932 73 11 0 3704 3776 661995791 661995863 2.340000e-09 75.0
31 TraesCS4A01G368300 chr1B 95.556 45 2 0 3732 3776 442964696 442964740 8.430000e-09 73.1
32 TraesCS4A01G368300 chr3A 99.470 944 4 1 5124 6066 501234627 501235570 0.000000e+00 1714.0
33 TraesCS4A01G368300 chrUn 93.915 871 45 6 2477 3343 384243015 384242149 0.000000e+00 1308.0
34 TraesCS4A01G368300 chrUn 96.780 559 18 0 3862 4420 473591782 473592340 0.000000e+00 933.0
35 TraesCS4A01G368300 chrUn 89.186 749 53 13 610 1351 256198517 256199244 0.000000e+00 909.0
36 TraesCS4A01G368300 chrUn 95.720 514 22 0 3347 3860 474648959 474648446 0.000000e+00 828.0
37 TraesCS4A01G368300 chrUn 87.121 660 32 14 4474 5124 175671433 175672048 0.000000e+00 699.0
38 TraesCS4A01G368300 chrUn 87.200 375 28 10 983 1351 175704756 175705116 5.660000e-110 409.0
39 TraesCS4A01G368300 chrUn 79.447 579 70 26 1833 2373 336623104 336622537 1.240000e-96 364.0
40 TraesCS4A01G368300 chrUn 78.209 592 69 27 1784 2362 354653608 354653064 2.110000e-84 324.0
41 TraesCS4A01G368300 chrUn 83.439 314 37 9 1046 1349 175733588 175733896 1.670000e-70 278.0
42 TraesCS4A01G368300 chrUn 79.392 296 37 17 2083 2362 256206653 256206940 2.890000e-43 187.0
43 TraesCS4A01G368300 chrUn 98.333 60 1 0 4422 4481 175665973 175666032 8.320000e-19 106.0
44 TraesCS4A01G368300 chrUn 87.324 71 5 1 646 716 175733522 175733588 1.810000e-10 78.7
45 TraesCS4A01G368300 chr5A 98.689 610 7 1 1 610 29611 30219 0.000000e+00 1081.0
46 TraesCS4A01G368300 chr5A 76.282 1813 386 34 2784 4580 29195361 29197145 0.000000e+00 926.0
47 TraesCS4A01G368300 chr1A 98.689 610 7 1 1 610 111984849 111985457 0.000000e+00 1081.0
48 TraesCS4A01G368300 chr7B 98.689 610 5 1 1 610 5928841 5929447 0.000000e+00 1079.0
49 TraesCS4A01G368300 chr7B 84.375 64 6 4 2358 2420 9104855 9104795 6.570000e-05 60.2
50 TraesCS4A01G368300 chr3B 97.848 604 12 1 1 604 647899147 647898545 0.000000e+00 1042.0
51 TraesCS4A01G368300 chr3B 93.617 47 3 0 4485 4531 584813556 584813602 3.030000e-08 71.3
52 TraesCS4A01G368300 chr6A 93.373 498 31 2 109 604 40918505 40919002 0.000000e+00 736.0
53 TraesCS4A01G368300 chr6A 93.750 80 5 0 1 80 40918424 40918503 2.970000e-23 121.0
54 TraesCS4A01G368300 chr4D 90.286 350 18 4 254 601 503520252 503520587 1.550000e-120 444.0
55 TraesCS4A01G368300 chr4D 87.004 277 27 8 75 343 188708025 188707750 2.750000e-78 303.0
56 TraesCS4A01G368300 chr2D 75.543 368 76 14 2873 3233 612365408 612365768 1.050000e-37 169.0
57 TraesCS4A01G368300 chr2D 91.489 47 4 0 4485 4531 612367091 612367137 1.410000e-06 65.8
58 TraesCS4A01G368300 chr2A 75.652 345 72 12 2895 3233 744492408 744492746 1.750000e-35 161.0
59 TraesCS4A01G368300 chr2A 80.952 84 16 0 4485 4568 744494056 744494139 3.920000e-07 67.6
60 TraesCS4A01G368300 chr6D 88.312 77 6 3 6 80 60310936 60311011 8.370000e-14 89.8
61 TraesCS4A01G368300 chr1D 84.932 73 11 0 3704 3776 475889380 475889452 2.340000e-09 75.0
62 TraesCS4A01G368300 chr1D 83.562 73 12 0 3704 3776 329488745 329488673 1.090000e-07 69.4


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 TraesCS4A01G368300 chr4A 641289836 641295901 6065 True 5289.500000 7910 100.000000 1 6066 2 chr4A.!!$R1 6065
1 TraesCS4A01G368300 chr4A 600963704 600964647 943 False 1744.000000 1744 100.000000 5123 6066 1 chr4A.!!$F2 943
2 TraesCS4A01G368300 chr5D 531287731 531293871 6140 False 1755.666667 3759 90.479333 610 5091 3 chr5D.!!$F2 4481
3 TraesCS4A01G368300 chr5D 40978621 40980405 1784 False 926.000000 926 76.309000 2784 4580 1 chr5D.!!$F1 1796
4 TraesCS4A01G368300 chr5B 6599816 6600759 943 True 1744.000000 1744 100.000000 5123 6066 1 chr5B.!!$R1 943
5 TraesCS4A01G368300 chr5B 480429557 480430506 949 False 1720.000000 1720 99.368000 5119 6066 1 chr5B.!!$F3 947
6 TraesCS4A01G368300 chr5B 35156097 35157872 1775 False 953.000000 953 76.620000 2784 4571 1 chr5B.!!$F2 1787
7 TraesCS4A01G368300 chr5B 35146892 35148654 1762 False 937.000000 937 76.680000 2784 4555 1 chr5B.!!$F1 1771
8 TraesCS4A01G368300 chr5B 670382939 670383651 712 False 905.000000 905 89.481000 623 1351 1 chr5B.!!$F4 728
9 TraesCS4A01G368300 chr5B 670437637 670438364 727 False 904.000000 904 89.052000 610 1351 1 chr5B.!!$F5 741
10 TraesCS4A01G368300 chr5B 670476483 670477098 615 False 688.000000 688 86.818000 4474 5124 1 chr5B.!!$F8 650
11 TraesCS4A01G368300 chr5B 670446476 670447031 555 False 361.000000 361 79.541000 1833 2362 1 chr5B.!!$F6 529
12 TraesCS4A01G368300 chr4B 37538114 37539056 942 True 1736.000000 1736 99.894000 5124 6066 1 chr4B.!!$R1 942
13 TraesCS4A01G368300 chr6B 129766107 129767049 942 False 1731.000000 1731 99.788000 5124 6066 1 chr6B.!!$F1 942
14 TraesCS4A01G368300 chr2B 62979340 62980288 948 False 1725.000000 1725 99.474000 5117 6066 1 chr2B.!!$F1 949
15 TraesCS4A01G368300 chr2B 587240291 587240865 574 False 1035.000000 1035 99.130000 1 575 1 chr2B.!!$F2 574
16 TraesCS4A01G368300 chr1B 15631160 15632102 942 False 1720.000000 1720 99.576000 5124 6066 1 chr1B.!!$F1 942
17 TraesCS4A01G368300 chr1B 431458936 431459878 942 False 1714.000000 1714 99.470000 5124 6066 1 chr1B.!!$F3 942
18 TraesCS4A01G368300 chr1B 16461583 16462191 608 False 1081.000000 1081 98.689000 1 610 1 chr1B.!!$F2 609
19 TraesCS4A01G368300 chr3A 501234627 501235570 943 False 1714.000000 1714 99.470000 5124 6066 1 chr3A.!!$F1 942
20 TraesCS4A01G368300 chrUn 384242149 384243015 866 True 1308.000000 1308 93.915000 2477 3343 1 chrUn.!!$R3 866
21 TraesCS4A01G368300 chrUn 473591782 473592340 558 False 933.000000 933 96.780000 3862 4420 1 chrUn.!!$F6 558
22 TraesCS4A01G368300 chrUn 256198517 256199244 727 False 909.000000 909 89.186000 610 1351 1 chrUn.!!$F4 741
23 TraesCS4A01G368300 chrUn 474648446 474648959 513 True 828.000000 828 95.720000 3347 3860 1 chrUn.!!$R4 513
24 TraesCS4A01G368300 chrUn 175671433 175672048 615 False 699.000000 699 87.121000 4474 5124 1 chrUn.!!$F2 650
25 TraesCS4A01G368300 chrUn 336622537 336623104 567 True 364.000000 364 79.447000 1833 2373 1 chrUn.!!$R1 540
26 TraesCS4A01G368300 chrUn 354653064 354653608 544 True 324.000000 324 78.209000 1784 2362 1 chrUn.!!$R2 578
27 TraesCS4A01G368300 chr5A 29611 30219 608 False 1081.000000 1081 98.689000 1 610 1 chr5A.!!$F1 609
28 TraesCS4A01G368300 chr5A 29195361 29197145 1784 False 926.000000 926 76.282000 2784 4580 1 chr5A.!!$F2 1796
29 TraesCS4A01G368300 chr1A 111984849 111985457 608 False 1081.000000 1081 98.689000 1 610 1 chr1A.!!$F1 609
30 TraesCS4A01G368300 chr7B 5928841 5929447 606 False 1079.000000 1079 98.689000 1 610 1 chr7B.!!$F1 609
31 TraesCS4A01G368300 chr3B 647898545 647899147 602 True 1042.000000 1042 97.848000 1 604 1 chr3B.!!$R1 603
32 TraesCS4A01G368300 chr6A 40918424 40919002 578 False 428.500000 736 93.561500 1 604 2 chr6A.!!$F1 603

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
680 684 0.250467 TGTCCAAGCTCAACTCCTGC 60.250 55.0 0.0 0.0 0.00 4.85 F
783 791 0.478507 CACTGGTTTCACTTCCCCCT 59.521 55.0 0.0 0.0 0.00 4.79 F
2187 3079 0.602562 AACCCCATGTGCATTTCGTG 59.397 50.0 0.0 0.0 0.00 4.35 F
2222 3116 0.463833 CCGCCTCCCCAACACTATTC 60.464 60.0 0.0 0.0 0.00 1.75 F
3592 5459 0.955428 GGCTCAAGACGAATGTGGCA 60.955 55.0 0.0 0.0 36.98 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2935 0.108963 TTTCGACACGGGTTGGGATT 59.891 50.000 4.91 0.00 0.0 3.01 R
2189 3081 0.602905 AGGCGGGAGTGAACTTTTCG 60.603 55.000 0.00 0.00 0.0 3.46 R
3265 5132 0.309302 CGGAGAGGAGCACGTAGATG 59.691 60.000 0.00 0.00 0.0 2.90 R
3626 5493 1.640069 CCGTCATGATTGCGAGCAG 59.360 57.895 0.00 0.00 0.0 4.24 R
5081 6965 0.236187 CTAGCTAGCTACGCGGACTG 59.764 60.000 20.67 4.73 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
581 585 2.278596 CCGCGACATACGACCAGG 60.279 66.667 8.23 0.00 45.77 4.45
647 651 1.592669 CATCGATCACCTCACCGCC 60.593 63.158 0.00 0.00 0.00 6.13
677 681 5.008118 GCTATATTTGTCCAAGCTCAACTCC 59.992 44.000 0.00 0.00 0.00 3.85
680 684 0.250467 TGTCCAAGCTCAACTCCTGC 60.250 55.000 0.00 0.00 0.00 4.85
692 698 1.545841 ACTCCTGCGTATGTGTGAGA 58.454 50.000 0.00 0.00 0.00 3.27
693 699 1.474478 ACTCCTGCGTATGTGTGAGAG 59.526 52.381 0.00 0.00 0.00 3.20
694 700 1.745653 CTCCTGCGTATGTGTGAGAGA 59.254 52.381 0.00 0.00 0.00 3.10
723 729 1.270839 CGGTTGAAGACCTGGTGACAT 60.271 52.381 2.82 0.00 46.92 3.06
729 735 1.885049 AGACCTGGTGACATAGCCAT 58.115 50.000 2.82 0.00 41.51 4.40
783 791 0.478507 CACTGGTTTCACTTCCCCCT 59.521 55.000 0.00 0.00 0.00 4.79
870 878 1.588404 GATCGACGATTGAACGCATGT 59.412 47.619 12.40 0.00 36.70 3.21
1263 1295 3.403038 GCTCACCGCCATTGAGTTATAT 58.597 45.455 5.92 0.00 42.26 0.86
1264 1296 3.187227 GCTCACCGCCATTGAGTTATATG 59.813 47.826 5.92 0.00 42.26 1.78
1265 1297 3.738982 TCACCGCCATTGAGTTATATGG 58.261 45.455 0.00 0.00 43.40 2.74
1266 1298 3.135712 TCACCGCCATTGAGTTATATGGT 59.864 43.478 0.00 0.00 42.67 3.55
1267 1299 3.882888 CACCGCCATTGAGTTATATGGTT 59.117 43.478 0.00 0.00 42.67 3.67
1268 1300 4.338118 CACCGCCATTGAGTTATATGGTTT 59.662 41.667 0.00 0.00 42.67 3.27
1269 1301 4.578928 ACCGCCATTGAGTTATATGGTTTC 59.421 41.667 0.00 0.00 42.67 2.78
1270 1302 4.319477 CCGCCATTGAGTTATATGGTTTCG 60.319 45.833 0.00 0.00 42.67 3.46
1271 1303 4.537015 GCCATTGAGTTATATGGTTTCGC 58.463 43.478 0.00 0.00 42.67 4.70
1272 1304 4.772434 CCATTGAGTTATATGGTTTCGCG 58.228 43.478 0.00 0.00 37.19 5.87
1273 1305 4.272504 CCATTGAGTTATATGGTTTCGCGT 59.727 41.667 5.77 0.00 37.19 6.01
1274 1306 4.850859 TTGAGTTATATGGTTTCGCGTG 57.149 40.909 5.77 0.00 0.00 5.34
1275 1307 2.605818 TGAGTTATATGGTTTCGCGTGC 59.394 45.455 5.77 0.00 0.00 5.34
1276 1308 2.864343 GAGTTATATGGTTTCGCGTGCT 59.136 45.455 5.77 0.00 0.00 4.40
1277 1309 3.267483 AGTTATATGGTTTCGCGTGCTT 58.733 40.909 5.77 0.00 0.00 3.91
1278 1310 4.435425 AGTTATATGGTTTCGCGTGCTTA 58.565 39.130 5.77 0.00 0.00 3.09
1279 1311 5.054477 AGTTATATGGTTTCGCGTGCTTAT 58.946 37.500 5.77 0.00 0.00 1.73
1280 1312 6.218019 AGTTATATGGTTTCGCGTGCTTATA 58.782 36.000 5.77 1.85 0.00 0.98
1281 1313 6.702723 AGTTATATGGTTTCGCGTGCTTATAA 59.297 34.615 5.77 5.61 0.00 0.98
1282 1314 7.386848 AGTTATATGGTTTCGCGTGCTTATAAT 59.613 33.333 5.77 0.00 0.00 1.28
1283 1315 8.649841 GTTATATGGTTTCGCGTGCTTATAATA 58.350 33.333 5.77 0.00 0.00 0.98
1284 1316 5.994887 ATGGTTTCGCGTGCTTATAATAA 57.005 34.783 5.77 0.00 0.00 1.40
1285 1317 5.798015 TGGTTTCGCGTGCTTATAATAAA 57.202 34.783 5.77 0.00 0.00 1.40
1286 1318 6.179504 TGGTTTCGCGTGCTTATAATAAAA 57.820 33.333 5.77 0.00 0.00 1.52
1287 1319 6.787225 TGGTTTCGCGTGCTTATAATAAAAT 58.213 32.000 5.77 0.00 0.00 1.82
1288 1320 7.917597 TGGTTTCGCGTGCTTATAATAAAATA 58.082 30.769 5.77 0.00 0.00 1.40
1289 1321 8.396390 TGGTTTCGCGTGCTTATAATAAAATAA 58.604 29.630 5.77 0.00 0.00 1.40
1290 1322 9.389570 GGTTTCGCGTGCTTATAATAAAATAAT 57.610 29.630 5.77 0.00 0.00 1.28
1316 1348 5.408299 TCACAATGTCACCTCGTCTATTTTG 59.592 40.000 0.00 0.00 0.00 2.44
1325 1377 5.920273 CACCTCGTCTATTTTGTTTTTGCAT 59.080 36.000 0.00 0.00 0.00 3.96
1362 1692 5.062934 CCATGAACATTATGCTTTGCAAGTG 59.937 40.000 0.00 0.00 43.62 3.16
1365 1695 6.743110 TGAACATTATGCTTTGCAAGTGTAA 58.257 32.000 0.00 0.00 43.62 2.41
1369 1699 8.606040 ACATTATGCTTTGCAAGTGTAAAAAT 57.394 26.923 0.00 0.00 43.62 1.82
1389 1719 2.180946 AGAGTGTGCCCATCTATCCA 57.819 50.000 0.00 0.00 0.00 3.41
1401 1731 6.006449 GCCCATCTATCCAATCACTGTTAAT 58.994 40.000 0.00 0.00 0.00 1.40
1416 1746 8.402798 TCACTGTTAATTTCATTGTGGTACAT 57.597 30.769 0.00 0.00 44.52 2.29
1813 2661 7.530010 CCTAATTTTGGGATGCGAGTAATATG 58.470 38.462 0.00 0.00 0.00 1.78
1820 2668 6.008331 TGGGATGCGAGTAATATGTACTACT 58.992 40.000 0.00 0.00 0.00 2.57
1821 2669 6.150641 TGGGATGCGAGTAATATGTACTACTC 59.849 42.308 9.06 9.06 40.36 2.59
1822 2670 6.404513 GGGATGCGAGTAATATGTACTACTCC 60.405 46.154 12.11 7.51 40.56 3.85
1823 2671 6.374894 GGATGCGAGTAATATGTACTACTCCT 59.625 42.308 12.11 1.46 40.56 3.69
1824 2672 7.551974 GGATGCGAGTAATATGTACTACTCCTA 59.448 40.741 12.11 4.74 40.56 2.94
1825 2673 7.664082 TGCGAGTAATATGTACTACTCCTAC 57.336 40.000 12.11 5.49 40.56 3.18
1895 2743 4.589908 CTGTAAGTAGGGGAGCAAAATGT 58.410 43.478 0.00 0.00 0.00 2.71
1973 2851 9.798994 ATGTGAGTAGAAGTTTATACGTTTAGG 57.201 33.333 0.00 0.00 30.58 2.69
2057 2935 6.984474 GTCCGACAACTATCCATTGAGATTTA 59.016 38.462 0.00 0.00 0.00 1.40
2068 2946 4.037923 CCATTGAGATTTAATCCCAACCCG 59.962 45.833 4.08 0.00 29.56 5.28
2071 2949 3.009695 TGAGATTTAATCCCAACCCGTGT 59.990 43.478 0.78 0.00 0.00 4.49
2073 2951 1.810959 TTTAATCCCAACCCGTGTCG 58.189 50.000 0.00 0.00 0.00 4.35
2092 2971 9.991388 CCGTGTCGAAATTTATAAAAATAAGGA 57.009 29.630 1.21 0.00 34.12 3.36
2186 3078 2.208132 TAACCCCATGTGCATTTCGT 57.792 45.000 0.00 0.00 0.00 3.85
2187 3079 0.602562 AACCCCATGTGCATTTCGTG 59.397 50.000 0.00 0.00 0.00 4.35
2189 3081 1.153784 CCCATGTGCATTTCGTGGC 60.154 57.895 8.25 0.00 39.76 5.01
2213 3107 4.649705 TTCACTCCCGCCTCCCCA 62.650 66.667 0.00 0.00 0.00 4.96
2222 3116 0.463833 CCGCCTCCCCAACACTATTC 60.464 60.000 0.00 0.00 0.00 1.75
2230 3124 6.525629 CCTCCCCAACACTATTCAGTTATAG 58.474 44.000 0.00 0.00 34.85 1.31
2274 3169 7.333174 TCAAACTGTTTTTGGAAGGACAAATTC 59.667 33.333 2.41 0.00 39.80 2.17
2284 3179 8.950007 TTGGAAGGACAAATTCTTACCTTAAT 57.050 30.769 0.00 0.00 40.42 1.40
2337 3232 5.042463 TGTTGGGTGAAGTGTATTCTTGA 57.958 39.130 0.00 0.00 0.00 3.02
2344 3239 8.160765 TGGGTGAAGTGTATTCTTGAGAATTTA 58.839 33.333 11.17 0.00 41.64 1.40
2415 3547 9.884814 ATTATAGTAATAGTGAACAGAGGGAGT 57.115 33.333 0.00 0.00 0.00 3.85
2418 3550 9.884814 ATAGTAATAGTGAACAGAGGGAGTATT 57.115 33.333 0.00 0.00 0.00 1.89
2480 4325 8.689251 AGTTTTAAGACTTTTGCTTGAAGTTC 57.311 30.769 0.00 0.00 37.46 3.01
2532 4377 4.442073 CACGCCAAAGTTTGATTTTCAGAG 59.558 41.667 17.33 2.95 0.00 3.35
2557 4402 1.464608 CCACCGTCTAATTGCAGTGTG 59.535 52.381 0.00 0.00 0.00 3.82
2560 4405 1.732259 CCGTCTAATTGCAGTGTGACC 59.268 52.381 8.51 0.00 0.00 4.02
2569 4414 2.013807 CAGTGTGACCGGTGTGTTG 58.986 57.895 14.63 0.00 0.00 3.33
2571 4416 1.153329 GTGTGACCGGTGTGTTGGA 60.153 57.895 14.63 0.00 0.00 3.53
2600 4445 2.873472 TGCGTTTGTAGTTCGAATGGTT 59.127 40.909 0.00 0.00 0.00 3.67
2626 4471 5.825679 TGGTAATGTCCAAATTAATCGGGAG 59.174 40.000 8.00 0.00 34.24 4.30
2651 4496 1.432514 CCATGTCGCCTATGGAATCG 58.567 55.000 6.57 0.00 46.42 3.34
2658 4503 2.557056 TCGCCTATGGAATCGAAGTAGG 59.443 50.000 0.00 0.00 35.98 3.18
2692 4538 5.125257 TCAAGCACTGTCAAATCAGTCAAAA 59.875 36.000 0.00 0.00 45.37 2.44
2693 4539 5.581126 AGCACTGTCAAATCAGTCAAAAA 57.419 34.783 0.00 0.00 45.37 1.94
2712 4561 8.919661 GTCAAAAATCACTTGATCAGAATTTCC 58.080 33.333 0.00 0.00 35.36 3.13
2717 4566 7.713734 ATCACTTGATCAGAATTTCCACATT 57.286 32.000 0.00 0.00 0.00 2.71
2735 4596 3.273434 CATTATGGGCATGTATCTCCGG 58.727 50.000 0.00 0.00 0.00 5.14
3087 4954 1.134818 CCCGTTCATCGTCTTCATGGA 60.135 52.381 0.00 0.00 37.94 3.41
3343 5210 1.821332 GCTGCTCCTGTACATGGCC 60.821 63.158 0.00 0.00 0.00 5.36
3592 5459 0.955428 GGCTCAAGACGAATGTGGCA 60.955 55.000 0.00 0.00 36.98 4.92
3599 5466 1.003580 AGACGAATGTGGCAACCATCT 59.996 47.619 0.00 0.00 35.28 2.90
3653 5520 2.835701 AATCATGACGGCGTGCGTCT 62.836 55.000 21.19 0.00 37.29 4.18
4663 6542 1.216977 CGACGAGGTGGCCATACAA 59.783 57.895 9.72 0.00 0.00 2.41
4673 6552 1.165270 GGCCATACAAAAGCACGTCT 58.835 50.000 0.00 0.00 0.00 4.18
4772 6651 1.584724 GAGGGGGAAGAATCTGGTGA 58.415 55.000 0.00 0.00 0.00 4.02
5032 6911 4.664677 ACGTCGCCTGGTGAGCAC 62.665 66.667 10.83 0.00 0.00 4.40
5092 6976 3.620428 CGCATGCAGTCCGCGTAG 61.620 66.667 19.57 0.00 46.97 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
571 575 1.829222 ACCGATTGTTCCTGGTCGTAT 59.171 47.619 0.00 0.00 32.55 3.06
581 585 6.259387 CCCTACTAATAAACCACCGATTGTTC 59.741 42.308 0.00 0.00 0.00 3.18
616 620 2.158608 TGATCGATGGAGCTCTGGACTA 60.159 50.000 14.64 0.00 0.00 2.59
647 651 2.631160 TGGACAAATATAGCCGGTGG 57.369 50.000 1.90 0.00 0.00 4.61
677 681 2.680339 TCTCTCTCTCACACATACGCAG 59.320 50.000 0.00 0.00 0.00 5.18
680 684 4.270084 GTCTCTCTCTCTCTCACACATACG 59.730 50.000 0.00 0.00 0.00 3.06
692 698 3.078837 GTCTTCAACCGTCTCTCTCTCT 58.921 50.000 0.00 0.00 0.00 3.10
693 699 2.162809 GGTCTTCAACCGTCTCTCTCTC 59.837 54.545 0.00 0.00 38.58 3.20
694 700 2.164338 GGTCTTCAACCGTCTCTCTCT 58.836 52.381 0.00 0.00 38.58 3.10
729 735 0.736636 CCGTGTGTCGAGTATGCCTA 59.263 55.000 0.00 0.00 42.86 3.93
783 791 0.679505 CGGAGGAACAAGTGGAGACA 59.320 55.000 0.00 0.00 38.70 3.41
918 926 0.904649 TGACCGGAGAGAACATGCAT 59.095 50.000 9.46 0.00 0.00 3.96
922 930 0.811915 CGTCTGACCGGAGAGAACAT 59.188 55.000 9.46 0.00 0.00 2.71
923 931 1.863662 GCGTCTGACCGGAGAGAACA 61.864 60.000 9.46 0.00 0.00 3.18
925 933 2.341101 GGCGTCTGACCGGAGAGAA 61.341 63.158 9.46 0.00 0.00 2.87
926 934 2.750637 GGCGTCTGACCGGAGAGA 60.751 66.667 9.46 5.65 0.00 3.10
927 935 3.057547 CTGGCGTCTGACCGGAGAG 62.058 68.421 9.46 2.74 35.38 3.20
1044 1052 2.436115 GCCTTCAGTGGCCGGTAC 60.436 66.667 1.90 2.66 46.82 3.34
1112 1120 4.598894 CAGGATGAGGAGCGGCCG 62.599 72.222 24.05 24.05 43.43 6.13
1113 1121 4.925861 GCAGGATGAGGAGCGGCC 62.926 72.222 0.00 0.00 39.69 6.13
1141 1149 4.308458 CGGGTGACGGCAAGGACA 62.308 66.667 0.00 0.00 39.42 4.02
1202 1210 4.142469 TGAACTTACGATGATCTCTGCGAA 60.142 41.667 0.00 0.00 0.00 4.70
1207 1215 6.322456 TGAGGAATGAACTTACGATGATCTCT 59.678 38.462 0.00 0.00 0.00 3.10
1250 1262 4.272504 ACGCGAAACCATATAACTCAATGG 59.727 41.667 15.93 0.00 46.76 3.16
1252 1264 4.260620 GCACGCGAAACCATATAACTCAAT 60.261 41.667 15.93 0.00 0.00 2.57
1263 1295 5.798015 TTTATTATAAGCACGCGAAACCA 57.202 34.783 15.93 0.00 0.00 3.67
1264 1296 8.770850 TTATTTTATTATAAGCACGCGAAACC 57.229 30.769 15.93 0.00 0.00 3.27
1266 1298 9.938670 ACATTATTTTATTATAAGCACGCGAAA 57.061 25.926 15.93 0.00 0.00 3.46
1267 1299 9.588774 GACATTATTTTATTATAAGCACGCGAA 57.411 29.630 15.93 0.00 0.00 4.70
1268 1300 8.766151 TGACATTATTTTATTATAAGCACGCGA 58.234 29.630 15.93 0.00 0.00 5.87
1269 1301 8.827599 GTGACATTATTTTATTATAAGCACGCG 58.172 33.333 3.53 3.53 0.00 6.01
1270 1302 9.658475 TGTGACATTATTTTATTATAAGCACGC 57.342 29.630 0.00 0.00 30.89 5.34
1281 1313 8.397906 CGAGGTGACATTGTGACATTATTTTAT 58.602 33.333 8.65 0.00 0.00 1.40
1282 1314 7.389330 ACGAGGTGACATTGTGACATTATTTTA 59.611 33.333 8.65 0.00 0.00 1.52
1283 1315 6.206634 ACGAGGTGACATTGTGACATTATTTT 59.793 34.615 8.65 0.00 0.00 1.82
1284 1316 5.705441 ACGAGGTGACATTGTGACATTATTT 59.295 36.000 8.65 0.00 0.00 1.40
1285 1317 5.245531 ACGAGGTGACATTGTGACATTATT 58.754 37.500 8.65 0.00 0.00 1.40
1286 1318 4.832248 ACGAGGTGACATTGTGACATTAT 58.168 39.130 8.65 0.00 0.00 1.28
1287 1319 4.021456 AGACGAGGTGACATTGTGACATTA 60.021 41.667 8.65 0.00 0.00 1.90
1288 1320 3.067106 GACGAGGTGACATTGTGACATT 58.933 45.455 8.65 0.00 0.00 2.71
1289 1321 2.300152 AGACGAGGTGACATTGTGACAT 59.700 45.455 8.65 0.52 0.00 3.06
1290 1322 1.686587 AGACGAGGTGACATTGTGACA 59.313 47.619 8.65 0.00 0.00 3.58
1316 1348 9.241317 CATGGACTAATTAGATCATGCAAAAAC 57.759 33.333 24.74 7.16 34.02 2.43
1362 1692 7.173390 GGATAGATGGGCACACTCTATTTTTAC 59.827 40.741 16.88 8.08 32.52 2.01
1365 1695 5.132648 TGGATAGATGGGCACACTCTATTTT 59.867 40.000 16.88 2.62 32.52 1.82
1369 1699 3.328535 TGGATAGATGGGCACACTCTA 57.671 47.619 0.00 0.00 0.00 2.43
1389 1719 8.855110 TGTACCACAATGAAATTAACAGTGATT 58.145 29.630 16.02 5.90 36.92 2.57
1799 2647 7.380431 AGGAGTAGTACATATTACTCGCATC 57.620 40.000 12.72 3.08 42.82 3.91
1813 2661 7.878547 ACTCAATTACTGGTAGGAGTAGTAC 57.121 40.000 0.00 0.00 34.13 2.73
1820 2668 5.546499 ACTCCAAACTCAATTACTGGTAGGA 59.454 40.000 0.00 0.00 0.00 2.94
1821 2669 5.805728 ACTCCAAACTCAATTACTGGTAGG 58.194 41.667 0.00 0.00 0.00 3.18
1822 2670 7.545965 CACTACTCCAAACTCAATTACTGGTAG 59.454 40.741 0.00 0.00 0.00 3.18
1823 2671 7.383687 CACTACTCCAAACTCAATTACTGGTA 58.616 38.462 0.00 0.00 0.00 3.25
1824 2672 6.231211 CACTACTCCAAACTCAATTACTGGT 58.769 40.000 0.00 0.00 0.00 4.00
1825 2673 5.122396 GCACTACTCCAAACTCAATTACTGG 59.878 44.000 0.00 0.00 0.00 4.00
2020 2898 8.895737 GGATAGTTGTCGGACCAAAATAAATAA 58.104 33.333 5.55 0.00 0.00 1.40
2057 2935 0.108963 TTTCGACACGGGTTGGGATT 59.891 50.000 4.91 0.00 0.00 3.01
2148 3029 9.603189 TGGGGTTAAAAATTTCAGGAATACTAA 57.397 29.630 0.00 0.00 0.00 2.24
2163 3044 4.202264 ACGAAATGCACATGGGGTTAAAAA 60.202 37.500 0.00 0.00 0.00 1.94
2171 3063 1.153784 GCCACGAAATGCACATGGG 60.154 57.895 0.00 0.00 0.00 4.00
2186 3078 0.882927 CGGGAGTGAACTTTTCGCCA 60.883 55.000 0.00 0.00 40.99 5.69
2187 3079 1.866925 CGGGAGTGAACTTTTCGCC 59.133 57.895 0.00 0.00 40.99 5.54
2189 3081 0.602905 AGGCGGGAGTGAACTTTTCG 60.603 55.000 0.00 0.00 0.00 3.46
2250 3145 7.394016 AGAATTTGTCCTTCCAAAAACAGTTT 58.606 30.769 0.00 0.00 37.81 2.66
2274 3169 8.360390 ACAGAGCTTTTGGAAAATTAAGGTAAG 58.640 33.333 0.00 0.00 0.00 2.34
2389 3521 9.884814 ACTCCCTCTGTTCACTATTACTATAAT 57.115 33.333 0.00 0.00 0.00 1.28
2392 3524 9.884814 AATACTCCCTCTGTTCACTATTACTAT 57.115 33.333 0.00 0.00 0.00 2.12
2393 3525 9.710818 AAATACTCCCTCTGTTCACTATTACTA 57.289 33.333 0.00 0.00 0.00 1.82
2394 3526 8.611051 AAATACTCCCTCTGTTCACTATTACT 57.389 34.615 0.00 0.00 0.00 2.24
2395 3527 9.668497 AAAAATACTCCCTCTGTTCACTATTAC 57.332 33.333 0.00 0.00 0.00 1.89
2422 4265 8.816894 GGTTCCTACCATCATATCTTGAGAATA 58.183 37.037 0.00 0.00 44.36 1.75
2439 4282 8.562892 GTCTTAAAACTACTTTTGGTTCCTACC 58.437 37.037 0.00 0.00 45.26 3.18
2453 4296 9.569167 AACTTCAAGCAAAAGTCTTAAAACTAC 57.431 29.630 0.00 0.00 35.96 2.73
2508 4353 4.111916 CTGAAAATCAAACTTTGGCGTGT 58.888 39.130 1.62 0.00 0.00 4.49
2532 4377 1.084289 GCAATTAGACGGTGGTGTCC 58.916 55.000 0.00 0.00 39.77 4.02
2557 4402 0.889186 AATGCTCCAACACACCGGTC 60.889 55.000 2.59 0.00 0.00 4.79
2560 4405 0.667993 ACAAATGCTCCAACACACCG 59.332 50.000 0.00 0.00 0.00 4.94
2626 4471 2.364324 TCCATAGGCGACATGGACTAAC 59.636 50.000 15.79 0.00 45.57 2.34
2639 4484 4.338379 AACCTACTTCGATTCCATAGGC 57.662 45.455 7.50 0.00 36.63 3.93
2651 4496 4.727475 GCTTGAGCATGAAAACCTACTTC 58.273 43.478 0.00 0.00 41.59 3.01
2692 4538 7.713734 ATGTGGAAATTCTGATCAAGTGATT 57.286 32.000 0.00 0.00 34.37 2.57
2693 4539 7.713734 AATGTGGAAATTCTGATCAAGTGAT 57.286 32.000 0.00 0.00 37.51 3.06
2712 4561 3.686241 CGGAGATACATGCCCATAATGTG 59.314 47.826 0.00 0.00 38.67 3.21
2717 4566 2.024176 ACCGGAGATACATGCCCATA 57.976 50.000 9.46 0.00 0.00 2.74
2722 4571 4.188247 TGCTATAACCGGAGATACATGC 57.812 45.455 9.46 5.86 0.00 4.06
2726 4575 4.566004 TGCATTGCTATAACCGGAGATAC 58.434 43.478 9.46 1.36 0.00 2.24
2735 4596 5.179045 ACATGAGCTTGCATTGCTATAAC 57.821 39.130 13.60 3.87 41.30 1.89
3018 4879 2.363147 GGAGCACGAGGGAGGAGT 60.363 66.667 0.00 0.00 0.00 3.85
3087 4954 3.440415 TGATGGAGAGCGCGACGT 61.440 61.111 12.10 0.00 0.00 4.34
3265 5132 0.309302 CGGAGAGGAGCACGTAGATG 59.691 60.000 0.00 0.00 0.00 2.90
3393 5260 1.728490 GGCAAGGACGATGGCCATTC 61.728 60.000 21.84 14.49 45.70 2.67
3394 5261 1.754234 GGCAAGGACGATGGCCATT 60.754 57.895 21.84 4.19 45.70 3.16
3592 5459 3.976701 CTTGGCGCCGGAGATGGTT 62.977 63.158 23.90 0.00 0.00 3.67
3626 5493 1.640069 CCGTCATGATTGCGAGCAG 59.360 57.895 0.00 0.00 0.00 4.24
3633 5500 2.021793 CGCACGCCGTCATGATTG 59.978 61.111 0.00 0.00 0.00 2.67
3653 5520 4.695993 TGTGCCGCCGATCTTGCA 62.696 61.111 5.15 0.00 0.00 4.08
4653 6532 0.878416 GACGTGCTTTTGTATGGCCA 59.122 50.000 8.56 8.56 0.00 5.36
4663 6542 2.032071 CCGGGGAAGACGTGCTTT 59.968 61.111 0.00 0.00 36.83 3.51
4691 6570 1.982395 CCACCACCTCCTCGTAGCA 60.982 63.158 0.00 0.00 0.00 3.49
4750 6629 1.700042 CCAGATTCTTCCCCCTCCCG 61.700 65.000 0.00 0.00 0.00 5.14
4859 6738 2.876645 CGTCGCCGAGAACTCTGC 60.877 66.667 7.89 7.89 36.63 4.26
4944 6823 3.522731 CTGCCTCCTCGTCCTCCG 61.523 72.222 0.00 0.00 38.13 4.63
4945 6824 2.043852 TCTGCCTCCTCGTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
4946 6825 2.124693 CCTCTGCCTCCTCGTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
4947 6826 2.043450 CCTCTGCCTCCTCGTCCT 60.043 66.667 0.00 0.00 0.00 3.85
4948 6827 2.043852 TCCTCTGCCTCCTCGTCC 60.044 66.667 0.00 0.00 0.00 4.79
4949 6828 1.679305 TGTCCTCTGCCTCCTCGTC 60.679 63.158 0.00 0.00 0.00 4.20
4950 6829 1.979693 GTGTCCTCTGCCTCCTCGT 60.980 63.158 0.00 0.00 0.00 4.18
4951 6830 1.943116 CTGTGTCCTCTGCCTCCTCG 61.943 65.000 0.00 0.00 0.00 4.63
4959 6838 1.665916 CGCACCACTGTGTCCTCTG 60.666 63.158 7.08 0.00 44.65 3.35
5032 6911 2.111878 CCTCCGGCTGGCCTATTG 59.888 66.667 6.73 0.00 34.14 1.90
5054 6933 4.824166 CGGCCGTCACGTACCGAG 62.824 72.222 20.99 0.00 43.79 4.63
5078 6962 1.360551 CTAGCTACGCGGACTGCAT 59.639 57.895 12.47 0.00 46.97 3.96
5079 6963 2.798689 CTAGCTACGCGGACTGCA 59.201 61.111 12.47 0.00 46.97 4.41
5080 6964 1.783031 TAGCTAGCTACGCGGACTGC 61.783 60.000 20.67 1.72 41.47 4.40
5081 6965 0.236187 CTAGCTAGCTACGCGGACTG 59.764 60.000 20.67 4.73 0.00 3.51
5082 6966 0.885596 CCTAGCTAGCTACGCGGACT 60.886 60.000 20.67 7.08 0.00 3.85
5083 6967 1.575423 CCTAGCTAGCTACGCGGAC 59.425 63.158 20.67 0.00 0.00 4.79
5084 6968 2.259439 GCCTAGCTAGCTACGCGGA 61.259 63.158 25.33 0.00 0.00 5.54
5085 6969 0.954449 TAGCCTAGCTAGCTACGCGG 60.954 60.000 28.56 24.29 41.83 6.46
5086 6970 2.541288 TAGCCTAGCTAGCTACGCG 58.459 57.895 28.56 17.49 41.83 6.01


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

AutoCloner maintained by Alex Coulton.