Multiple sequence alignment - TraesCS6D01G349100

Loading Multiple Alignment...

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 TraesCS6D01G349100 chr6D 100.000 2513 0 0 1 2513 446933814 446936326 0.000000e+00 4641.0
1 TraesCS6D01G349100 chr6D 98.592 426 6 0 318 743 155256129 155255704 0.000000e+00 754.0
2 TraesCS6D01G349100 chr6D 88.889 495 40 7 995 1489 446902023 446902502 1.660000e-166 595.0
3 TraesCS6D01G349100 chr6D 77.756 998 122 44 995 1946 446882320 446883263 2.860000e-144 521.0
4 TraesCS6D01G349100 chr6D 98.134 268 5 0 1 268 155256881 155256614 3.780000e-128 468.0
5 TraesCS6D01G349100 chr6D 84.400 500 35 13 995 1489 446948451 446948912 3.810000e-123 451.0
6 TraesCS6D01G349100 chr6D 85.424 295 36 4 1697 1988 447277809 447277519 1.460000e-77 300.0
7 TraesCS6D01G349100 chr6A 86.914 1345 105 35 880 2206 593785619 593786910 0.000000e+00 1443.0
8 TraesCS6D01G349100 chr6A 87.114 551 48 12 992 1542 593777184 593777711 9.940000e-169 603.0
9 TraesCS6D01G349100 chr6A 82.903 503 40 26 995 1489 593792305 593792769 6.470000e-111 411.0
10 TraesCS6D01G349100 chr6A 90.323 279 10 9 2226 2490 593787022 593787297 1.430000e-92 350.0
11 TraesCS6D01G349100 chr6A 97.561 41 1 0 2390 2430 593778789 593778829 1.250000e-08 71.3
12 TraesCS6D01G349100 chr6A 97.368 38 1 0 2393 2430 594368683 594368720 5.800000e-07 65.8
13 TraesCS6D01G349100 chr6B 88.480 1059 80 20 951 2000 676123537 676124562 0.000000e+00 1242.0
14 TraesCS6D01G349100 chr6B 87.659 551 49 11 995 1545 675626739 675626208 7.630000e-175 623.0
15 TraesCS6D01G349100 chr6B 81.517 633 62 37 863 1489 676136267 676136850 1.050000e-128 470.0
16 TraesCS6D01G349100 chr6B 76.436 1027 114 72 958 1946 676036407 676037343 2.970000e-119 438.0
17 TraesCS6D01G349100 chr6B 83.000 500 45 24 995 1492 675568471 675568010 1.390000e-112 416.0
18 TraesCS6D01G349100 chr6B 91.011 267 21 3 1647 1912 675612853 675612589 8.550000e-95 357.0
19 TraesCS6D01G349100 chr6B 85.172 290 13 8 852 1141 675614528 675614269 1.150000e-68 270.0
20 TraesCS6D01G349100 chr6B 80.155 388 50 12 1630 1996 677087549 677087168 5.330000e-67 265.0
21 TraesCS6D01G349100 chr6B 82.848 309 39 7 1697 1996 678175646 678175949 5.330000e-67 265.0
22 TraesCS6D01G349100 chr6B 81.988 322 44 7 995 1312 676047369 676047680 6.890000e-66 261.0
23 TraesCS6D01G349100 chr6B 79.897 388 50 13 1630 1996 677777750 677777370 2.480000e-65 259.0
24 TraesCS6D01G349100 chr6B 79.897 388 51 12 1630 1996 677910031 677909650 2.480000e-65 259.0
25 TraesCS6D01G349100 chr6B 84.942 259 20 3 2229 2471 675612265 675612010 6.940000e-61 244.0
26 TraesCS6D01G349100 chr6B 81.231 325 39 11 1682 1997 676536732 676536421 2.500000e-60 243.0
27 TraesCS6D01G349100 chr6B 90.816 98 9 0 2333 2430 675609767 675609670 5.640000e-27 132.0
28 TraesCS6D01G349100 chr6B 88.571 105 11 1 2083 2187 675612471 675612368 2.620000e-25 126.0
29 TraesCS6D01G349100 chr6B 93.548 62 4 0 858 919 676123470 676123531 2.660000e-15 93.5
30 TraesCS6D01G349100 chr6B 81.905 105 10 5 2335 2430 678544193 678544297 2.070000e-11 80.5
31 TraesCS6D01G349100 chr6B 77.181 149 16 9 2332 2462 676728695 676728547 1.250000e-08 71.3
32 TraesCS6D01G349100 chr7D 93.544 759 25 4 1 743 40193361 40192611 0.000000e+00 1109.0
33 TraesCS6D01G349100 chr5D 96.398 472 9 1 273 744 210380716 210380253 0.000000e+00 771.0
34 TraesCS6D01G349100 chr5D 98.326 239 4 0 1 239 210381440 210381202 1.070000e-113 420.0
35 TraesCS6D01G349100 chr5D 85.281 231 25 7 9 230 69937624 69937854 1.940000e-56 230.0
36 TraesCS6D01G349100 chr5D 100.000 35 0 0 2 36 69937638 69937672 5.800000e-07 65.8
37 TraesCS6D01G349100 chr3A 88.247 485 36 6 175 656 657389619 657390085 6.070000e-156 560.0
38 TraesCS6D01G349100 chr3A 93.791 306 18 1 2 307 657389369 657389673 2.280000e-125 459.0
39 TraesCS6D01G349100 chr7B 84.035 570 43 18 177 743 743770967 743770443 2.880000e-139 505.0
40 TraesCS6D01G349100 chr7B 87.879 297 32 4 14 309 743771259 743770966 1.850000e-91 346.0
41 TraesCS6D01G349100 chr4B 87.838 444 31 11 310 743 54943670 54943240 1.340000e-137 499.0
42 TraesCS6D01G349100 chr2B 83.077 585 54 14 175 743 673109778 673109223 8.080000e-135 490.0
43 TraesCS6D01G349100 chr2B 87.671 292 32 4 2 292 673110053 673109765 1.110000e-88 337.0
44 TraesCS6D01G349100 chrUn 85.217 115 10 5 561 674 64206048 64205940 7.350000e-21 111.0


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 TraesCS6D01G349100 chr6D 446933814 446936326 2512 False 4641.00 4641 100.0000 1 2513 1 chr6D.!!$F3 2512
1 TraesCS6D01G349100 chr6D 155255704 155256881 1177 True 611.00 754 98.3630 1 743 2 chr6D.!!$R2 742
2 TraesCS6D01G349100 chr6D 446882320 446883263 943 False 521.00 521 77.7560 995 1946 1 chr6D.!!$F1 951
3 TraesCS6D01G349100 chr6A 593785619 593787297 1678 False 896.50 1443 88.6185 880 2490 2 chr6A.!!$F4 1610
4 TraesCS6D01G349100 chr6A 593777184 593778829 1645 False 337.15 603 92.3375 992 2430 2 chr6A.!!$F3 1438
5 TraesCS6D01G349100 chr6B 676123470 676124562 1092 False 667.75 1242 91.0140 858 2000 2 chr6B.!!$F6 1142
6 TraesCS6D01G349100 chr6B 675626208 675626739 531 True 623.00 623 87.6590 995 1545 1 chr6B.!!$R2 550
7 TraesCS6D01G349100 chr6B 676136267 676136850 583 False 470.00 470 81.5170 863 1489 1 chr6B.!!$F3 626
8 TraesCS6D01G349100 chr6B 676036407 676037343 936 False 438.00 438 76.4360 958 1946 1 chr6B.!!$F1 988
9 TraesCS6D01G349100 chr6B 675609670 675614528 4858 True 225.80 357 88.1024 852 2471 5 chr6B.!!$R8 1619
10 TraesCS6D01G349100 chr7D 40192611 40193361 750 True 1109.00 1109 93.5440 1 743 1 chr7D.!!$R1 742
11 TraesCS6D01G349100 chr5D 210380253 210381440 1187 True 595.50 771 97.3620 1 744 2 chr5D.!!$R1 743
12 TraesCS6D01G349100 chr3A 657389369 657390085 716 False 509.50 560 91.0190 2 656 2 chr3A.!!$F1 654
13 TraesCS6D01G349100 chr7B 743770443 743771259 816 True 425.50 505 85.9570 14 743 2 chr7B.!!$R1 729
14 TraesCS6D01G349100 chr2B 673109223 673110053 830 True 413.50 490 85.3740 2 743 2 chr2B.!!$R1 741

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
784 1366 0.032403 CACGTGTCAGGGTCCGTAAA 59.968 55.0 7.58 0.0 31.42 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 3750 0.034896 ACGGATCCACAGTTCCACAC 59.965 55.0 13.41 0.0 32.13 3.82 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
440 1003 2.042464 CAGGAGGGGATCGAGAATTCA 58.958 52.381 8.44 0.00 0.00 2.57
609 1176 1.352622 ATATTGAAGCCCAGGCCCGA 61.353 55.000 4.70 0.00 43.17 5.14
744 1326 1.444933 TTCCCATGGCCAGGTATAGG 58.555 55.000 17.55 10.41 0.00 2.57
745 1327 0.475632 TCCCATGGCCAGGTATAGGG 60.476 60.000 17.55 16.60 36.15 3.53
746 1328 1.500783 CCCATGGCCAGGTATAGGGG 61.501 65.000 17.55 11.35 0.00 4.79
747 1329 1.500783 CCATGGCCAGGTATAGGGGG 61.501 65.000 17.55 0.00 0.00 5.40
764 1346 2.073252 GGGGGCAAATTAGAGAAGGG 57.927 55.000 0.00 0.00 0.00 3.95
765 1347 1.403814 GGGGCAAATTAGAGAAGGGC 58.596 55.000 0.00 0.00 0.00 5.19
766 1348 1.341976 GGGGCAAATTAGAGAAGGGCA 60.342 52.381 0.00 0.00 0.00 5.36
767 1349 1.751351 GGGCAAATTAGAGAAGGGCAC 59.249 52.381 0.00 0.00 0.00 5.01
768 1350 1.401905 GGCAAATTAGAGAAGGGCACG 59.598 52.381 0.00 0.00 0.00 5.34
769 1351 2.084546 GCAAATTAGAGAAGGGCACGT 58.915 47.619 0.00 0.00 0.00 4.49
770 1352 2.159517 GCAAATTAGAGAAGGGCACGTG 60.160 50.000 12.28 12.28 0.00 4.49
771 1353 3.074412 CAAATTAGAGAAGGGCACGTGT 58.926 45.455 18.38 0.00 0.00 4.49
772 1354 2.674796 ATTAGAGAAGGGCACGTGTC 57.325 50.000 18.38 15.79 0.00 3.67
773 1355 1.334160 TTAGAGAAGGGCACGTGTCA 58.666 50.000 23.45 0.00 0.00 3.58
774 1356 0.888619 TAGAGAAGGGCACGTGTCAG 59.111 55.000 23.45 0.00 0.00 3.51
775 1357 1.374758 GAGAAGGGCACGTGTCAGG 60.375 63.158 23.45 0.00 0.00 3.86
776 1358 2.358737 GAAGGGCACGTGTCAGGG 60.359 66.667 23.45 0.00 0.00 4.45
777 1359 3.168528 AAGGGCACGTGTCAGGGT 61.169 61.111 23.45 0.00 0.00 4.34
778 1360 3.178540 AAGGGCACGTGTCAGGGTC 62.179 63.158 23.45 3.62 0.00 4.46
779 1361 4.699522 GGGCACGTGTCAGGGTCC 62.700 72.222 23.45 10.02 29.09 4.46
781 1363 4.295119 GCACGTGTCAGGGTCCGT 62.295 66.667 18.38 0.00 0.00 4.69
782 1364 2.922950 GCACGTGTCAGGGTCCGTA 61.923 63.158 18.38 0.00 31.42 4.02
783 1365 1.661480 CACGTGTCAGGGTCCGTAA 59.339 57.895 7.58 0.00 31.42 3.18
784 1366 0.032403 CACGTGTCAGGGTCCGTAAA 59.968 55.000 7.58 0.00 31.42 2.01
785 1367 0.752054 ACGTGTCAGGGTCCGTAAAA 59.248 50.000 0.00 0.00 0.00 1.52
786 1368 1.269936 ACGTGTCAGGGTCCGTAAAAG 60.270 52.381 0.00 0.00 0.00 2.27
787 1369 1.269936 CGTGTCAGGGTCCGTAAAAGT 60.270 52.381 0.00 0.00 0.00 2.66
788 1370 2.410939 GTGTCAGGGTCCGTAAAAGTC 58.589 52.381 0.00 0.00 0.00 3.01
789 1371 1.345415 TGTCAGGGTCCGTAAAAGTCC 59.655 52.381 0.00 0.00 0.00 3.85
790 1372 0.604578 TCAGGGTCCGTAAAAGTCCG 59.395 55.000 0.00 0.00 0.00 4.79
791 1373 0.319405 CAGGGTCCGTAAAAGTCCGT 59.681 55.000 0.00 0.00 0.00 4.69
792 1374 0.605083 AGGGTCCGTAAAAGTCCGTC 59.395 55.000 0.00 0.00 0.00 4.79
793 1375 0.733909 GGGTCCGTAAAAGTCCGTCG 60.734 60.000 0.00 0.00 0.00 5.12
794 1376 0.240945 GGTCCGTAAAAGTCCGTCGA 59.759 55.000 0.00 0.00 0.00 4.20
795 1377 1.611043 GTCCGTAAAAGTCCGTCGAG 58.389 55.000 0.00 0.00 0.00 4.04
796 1378 1.197721 GTCCGTAAAAGTCCGTCGAGA 59.802 52.381 0.00 0.00 0.00 4.04
797 1379 1.466167 TCCGTAAAAGTCCGTCGAGAG 59.534 52.381 0.00 0.00 0.00 3.20
798 1380 1.466167 CCGTAAAAGTCCGTCGAGAGA 59.534 52.381 0.00 0.00 38.16 3.10
799 1381 2.475852 CCGTAAAAGTCCGTCGAGAGAG 60.476 54.545 0.00 0.00 43.49 3.20
800 1382 2.517935 GTAAAAGTCCGTCGAGAGAGC 58.482 52.381 0.00 0.00 43.49 4.09
801 1383 0.244178 AAAAGTCCGTCGAGAGAGCC 59.756 55.000 0.00 0.00 43.49 4.70
802 1384 1.596895 AAAGTCCGTCGAGAGAGCCC 61.597 60.000 0.00 0.00 43.49 5.19
803 1385 3.878519 GTCCGTCGAGAGAGCCCG 61.879 72.222 0.00 0.00 43.49 6.13
804 1386 4.405671 TCCGTCGAGAGAGCCCGT 62.406 66.667 0.00 0.00 43.49 5.28
805 1387 4.180946 CCGTCGAGAGAGCCCGTG 62.181 72.222 0.00 0.00 43.49 4.94
806 1388 3.432588 CGTCGAGAGAGCCCGTGT 61.433 66.667 0.00 0.00 43.49 4.49
807 1389 2.179517 GTCGAGAGAGCCCGTGTG 59.820 66.667 0.00 0.00 43.49 3.82
808 1390 2.282251 TCGAGAGAGCCCGTGTGT 60.282 61.111 0.00 0.00 34.84 3.72
809 1391 2.126307 CGAGAGAGCCCGTGTGTG 60.126 66.667 0.00 0.00 0.00 3.82
810 1392 2.920645 CGAGAGAGCCCGTGTGTGT 61.921 63.158 0.00 0.00 0.00 3.72
811 1393 1.583495 CGAGAGAGCCCGTGTGTGTA 61.583 60.000 0.00 0.00 0.00 2.90
812 1394 0.171455 GAGAGAGCCCGTGTGTGTAG 59.829 60.000 0.00 0.00 0.00 2.74
813 1395 0.539901 AGAGAGCCCGTGTGTGTAGT 60.540 55.000 0.00 0.00 0.00 2.73
814 1396 1.171308 GAGAGCCCGTGTGTGTAGTA 58.829 55.000 0.00 0.00 0.00 1.82
815 1397 1.749634 GAGAGCCCGTGTGTGTAGTAT 59.250 52.381 0.00 0.00 0.00 2.12
816 1398 2.165845 GAGAGCCCGTGTGTGTAGTATT 59.834 50.000 0.00 0.00 0.00 1.89
817 1399 3.359033 AGAGCCCGTGTGTGTAGTATTA 58.641 45.455 0.00 0.00 0.00 0.98
818 1400 3.958798 AGAGCCCGTGTGTGTAGTATTAT 59.041 43.478 0.00 0.00 0.00 1.28
819 1401 4.037684 AGAGCCCGTGTGTGTAGTATTATC 59.962 45.833 0.00 0.00 0.00 1.75
820 1402 3.047796 GCCCGTGTGTGTAGTATTATCG 58.952 50.000 0.00 0.00 0.00 2.92
821 1403 3.489738 GCCCGTGTGTGTAGTATTATCGT 60.490 47.826 0.00 0.00 0.00 3.73
822 1404 4.675510 CCCGTGTGTGTAGTATTATCGTT 58.324 43.478 0.00 0.00 0.00 3.85
823 1405 5.104374 CCCGTGTGTGTAGTATTATCGTTT 58.896 41.667 0.00 0.00 0.00 3.60
824 1406 5.230726 CCCGTGTGTGTAGTATTATCGTTTC 59.769 44.000 0.00 0.00 0.00 2.78
825 1407 6.032094 CCGTGTGTGTAGTATTATCGTTTCT 58.968 40.000 0.00 0.00 0.00 2.52
826 1408 6.195983 CCGTGTGTGTAGTATTATCGTTTCTC 59.804 42.308 0.00 0.00 0.00 2.87
827 1409 6.195983 CGTGTGTGTAGTATTATCGTTTCTCC 59.804 42.308 0.00 0.00 0.00 3.71
828 1410 6.474751 GTGTGTGTAGTATTATCGTTTCTCCC 59.525 42.308 0.00 0.00 0.00 4.30
829 1411 5.981915 GTGTGTAGTATTATCGTTTCTCCCC 59.018 44.000 0.00 0.00 0.00 4.81
830 1412 5.069516 TGTGTAGTATTATCGTTTCTCCCCC 59.930 44.000 0.00 0.00 0.00 5.40
831 1413 5.069516 GTGTAGTATTATCGTTTCTCCCCCA 59.930 44.000 0.00 0.00 0.00 4.96
832 1414 5.842328 TGTAGTATTATCGTTTCTCCCCCAT 59.158 40.000 0.00 0.00 0.00 4.00
833 1415 5.228945 AGTATTATCGTTTCTCCCCCATG 57.771 43.478 0.00 0.00 0.00 3.66
834 1416 2.341846 TTATCGTTTCTCCCCCATGC 57.658 50.000 0.00 0.00 0.00 4.06
835 1417 1.208706 TATCGTTTCTCCCCCATGCA 58.791 50.000 0.00 0.00 0.00 3.96
836 1418 0.331278 ATCGTTTCTCCCCCATGCAA 59.669 50.000 0.00 0.00 0.00 4.08
837 1419 0.111446 TCGTTTCTCCCCCATGCAAA 59.889 50.000 0.00 0.00 0.00 3.68
838 1420 0.965439 CGTTTCTCCCCCATGCAAAA 59.035 50.000 0.00 0.00 0.00 2.44
839 1421 1.342819 CGTTTCTCCCCCATGCAAAAA 59.657 47.619 0.00 0.00 0.00 1.94
942 1525 4.659172 TCCCCCAAACCAGCAGCG 62.659 66.667 0.00 0.00 0.00 5.18
946 1549 1.535204 CCCCAAACCAGCAGCGAAAT 61.535 55.000 0.00 0.00 0.00 2.17
948 1551 0.883833 CCAAACCAGCAGCGAAATCT 59.116 50.000 0.00 0.00 0.00 2.40
952 1555 0.254178 ACCAGCAGCGAAATCTCCAT 59.746 50.000 0.00 0.00 0.00 3.41
956 1559 0.305922 GCAGCGAAATCTCCATTCCG 59.694 55.000 0.00 0.00 0.00 4.30
973 1576 2.165301 CGACCCGATTCCAACGCTC 61.165 63.158 0.00 0.00 0.00 5.03
987 1590 2.026879 GCTCGCACTCCTCGATCC 59.973 66.667 0.00 0.00 35.25 3.36
989 1592 1.809869 CTCGCACTCCTCGATCCAA 59.190 57.895 0.00 0.00 35.25 3.53
990 1593 0.248825 CTCGCACTCCTCGATCCAAG 60.249 60.000 0.00 0.00 35.25 3.61
1005 1609 1.003580 TCCAAGTGTTCTCTCATGGCC 59.996 52.381 0.00 0.00 0.00 5.36
1025 1629 3.827898 GGCGACTGCGAGTAGGCT 61.828 66.667 12.76 0.00 41.80 4.58
1271 1931 2.751436 GGCGGCTCCATCTTGCAA 60.751 61.111 0.00 0.00 34.01 4.08
1610 3189 1.533711 CCAATTCTGGGATCCGGCT 59.466 57.895 5.45 0.00 39.30 5.52
1635 3214 4.158025 GGCCAATTAGCTAGCTCGTAGATA 59.842 45.833 23.26 0.00 33.89 1.98
1636 3215 5.336744 GCCAATTAGCTAGCTCGTAGATAG 58.663 45.833 23.26 5.08 37.28 2.08
1639 3224 6.373216 CCAATTAGCTAGCTCGTAGATAGAGT 59.627 42.308 23.26 0.00 36.36 3.24
1640 3225 6.978343 ATTAGCTAGCTCGTAGATAGAGTG 57.022 41.667 23.26 0.00 36.36 3.51
1645 3254 2.500229 GCTCGTAGATAGAGTGAGCCT 58.500 52.381 1.21 0.00 44.76 4.58
1653 3262 1.919240 TAGAGTGAGCCTTTCGTCCA 58.081 50.000 0.00 0.00 0.00 4.02
1659 3268 0.318762 GAGCCTTTCGTCCACTCTGT 59.681 55.000 0.00 0.00 0.00 3.41
1678 3287 2.169561 TGTTCTGCTGTGTACAACTCCA 59.830 45.455 0.00 0.00 0.00 3.86
1722 3349 5.233083 TCATGAGTGACAAATTGGAGACT 57.767 39.130 0.00 0.00 0.00 3.24
1723 3350 4.999311 TCATGAGTGACAAATTGGAGACTG 59.001 41.667 0.00 0.00 0.00 3.51
1902 3576 3.639541 CTCGCTGTCGCTTGCTCCT 62.640 63.158 0.00 0.00 35.26 3.69
1915 3589 2.991076 GCTCCTGTCACGCGGTACT 61.991 63.158 12.47 0.00 0.00 2.73
1947 3621 4.162690 GCCGAACGGATCAGGCCT 62.163 66.667 17.63 0.00 39.97 5.19
1949 3623 2.579201 CGAACGGATCAGGCCTGT 59.421 61.111 31.58 19.20 0.00 4.00
1962 3646 0.960861 GGCCTGTAACTTGGAGCACC 60.961 60.000 0.00 0.00 0.00 5.01
2007 3691 9.763465 CGACGAGGTTTATGTATGTAAAATTTT 57.237 29.630 8.75 8.75 0.00 1.82
2028 3712 1.500474 TGATCCCAGTCCCAGTGATC 58.500 55.000 0.00 0.00 33.96 2.92
2031 3715 0.984230 TCCCAGTCCCAGTGATCAAC 59.016 55.000 0.00 0.00 0.00 3.18
2048 3738 0.600255 AACGAAGTGAGGCTGAACCG 60.600 55.000 0.00 0.00 45.00 4.44
2053 3743 1.557099 AGTGAGGCTGAACCGATGTA 58.443 50.000 0.00 0.00 46.52 2.29
2054 3744 1.204941 AGTGAGGCTGAACCGATGTAC 59.795 52.381 0.00 0.00 46.52 2.90
2056 3746 1.204704 TGAGGCTGAACCGATGTACTG 59.795 52.381 0.00 0.00 46.52 2.74
2058 3748 1.066858 AGGCTGAACCGATGTACTGTG 60.067 52.381 0.00 0.00 46.52 3.66
2060 3750 1.726791 GCTGAACCGATGTACTGTGTG 59.273 52.381 0.00 0.00 0.00 3.82
2062 3752 2.731451 CTGAACCGATGTACTGTGTGTG 59.269 50.000 0.00 0.00 0.00 3.82
2063 3753 2.101750 TGAACCGATGTACTGTGTGTGT 59.898 45.455 0.00 0.00 0.00 3.72
2064 3754 2.148916 ACCGATGTACTGTGTGTGTG 57.851 50.000 0.00 0.00 0.00 3.82
2065 3755 1.270094 ACCGATGTACTGTGTGTGTGG 60.270 52.381 0.00 0.00 0.00 4.17
2066 3756 1.000394 CCGATGTACTGTGTGTGTGGA 60.000 52.381 0.00 0.00 0.00 4.02
2067 3757 2.547007 CCGATGTACTGTGTGTGTGGAA 60.547 50.000 0.00 0.00 0.00 3.53
2068 3758 2.475111 CGATGTACTGTGTGTGTGGAAC 59.525 50.000 0.00 0.00 37.35 3.62
2069 3759 3.728845 GATGTACTGTGTGTGTGGAACT 58.271 45.455 0.00 0.00 38.04 3.01
2071 3761 2.235155 TGTACTGTGTGTGTGGAACTGT 59.765 45.455 0.00 0.00 38.04 3.55
2072 3762 1.737838 ACTGTGTGTGTGGAACTGTG 58.262 50.000 0.00 0.00 38.04 3.66
2073 3763 1.016627 CTGTGTGTGTGGAACTGTGG 58.983 55.000 0.00 0.00 38.04 4.17
2074 3764 0.615850 TGTGTGTGTGGAACTGTGGA 59.384 50.000 0.00 0.00 38.04 4.02
2076 3766 1.873591 GTGTGTGTGGAACTGTGGATC 59.126 52.381 0.00 0.00 38.04 3.36
2077 3767 1.202758 TGTGTGTGGAACTGTGGATCC 60.203 52.381 4.20 4.20 38.04 3.36
2078 3768 0.034756 TGTGTGGAACTGTGGATCCG 59.965 55.000 7.39 0.00 37.24 4.18
2079 3769 0.034896 GTGTGGAACTGTGGATCCGT 59.965 55.000 7.39 0.00 37.24 4.69
2080 3770 0.034756 TGTGGAACTGTGGATCCGTG 59.965 55.000 7.39 2.00 37.24 4.94
2099 3791 1.813786 TGGTATTTTACTGTTGGCGCC 59.186 47.619 22.73 22.73 0.00 6.53
2101 3793 2.159435 GGTATTTTACTGTTGGCGCCAG 60.159 50.000 30.75 20.97 36.01 4.85
2222 3995 2.487934 TGTCTCTCTTTCAAGTGCAGC 58.512 47.619 0.00 0.00 0.00 5.25
2337 4235 1.806542 GTATGAACAGCCGGCATATGG 59.193 52.381 31.54 14.61 0.00 2.74
2344 4242 1.302511 GCCGGCATATGGGTCGAAT 60.303 57.895 24.80 0.00 38.35 3.34
2383 4283 0.764369 AGTGGAGTTGCTGGGAGTGA 60.764 55.000 0.00 0.00 0.00 3.41
2470 4395 2.125512 AGACGGGCATTCGCAGAC 60.126 61.111 0.00 0.00 41.24 3.51
2490 4415 2.979678 ACCCAAAGTAGAAGCTCTGGAA 59.020 45.455 0.00 0.00 0.00 3.53
2491 4416 3.244596 ACCCAAAGTAGAAGCTCTGGAAC 60.245 47.826 0.00 0.00 0.00 3.62
2501 4426 3.966026 CTCTGGAACGACGACGGCC 62.966 68.421 12.58 12.67 44.46 6.13
2505 4430 4.093952 GAACGACGACGGCCGAGA 62.094 66.667 35.90 0.00 44.46 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
440 1003 3.411517 CTCCCACGCCCCCATCTT 61.412 66.667 0.00 0.00 0.00 2.40
745 1327 2.029520 GCCCTTCTCTAATTTGCCCCC 61.030 57.143 0.00 0.00 0.00 5.40
746 1328 1.341976 TGCCCTTCTCTAATTTGCCCC 60.342 52.381 0.00 0.00 0.00 5.80
747 1329 1.751351 GTGCCCTTCTCTAATTTGCCC 59.249 52.381 0.00 0.00 0.00 5.36
748 1330 1.401905 CGTGCCCTTCTCTAATTTGCC 59.598 52.381 0.00 0.00 0.00 4.52
749 1331 2.084546 ACGTGCCCTTCTCTAATTTGC 58.915 47.619 0.00 0.00 0.00 3.68
750 1332 3.074412 ACACGTGCCCTTCTCTAATTTG 58.926 45.455 17.22 0.00 0.00 2.32
751 1333 3.244422 TGACACGTGCCCTTCTCTAATTT 60.244 43.478 17.22 0.00 0.00 1.82
752 1334 2.301870 TGACACGTGCCCTTCTCTAATT 59.698 45.455 17.22 0.00 0.00 1.40
753 1335 1.899814 TGACACGTGCCCTTCTCTAAT 59.100 47.619 17.22 0.00 0.00 1.73
754 1336 1.272490 CTGACACGTGCCCTTCTCTAA 59.728 52.381 17.22 0.00 0.00 2.10
755 1337 0.888619 CTGACACGTGCCCTTCTCTA 59.111 55.000 17.22 0.00 0.00 2.43
756 1338 1.668294 CTGACACGTGCCCTTCTCT 59.332 57.895 17.22 0.00 0.00 3.10
757 1339 1.374758 CCTGACACGTGCCCTTCTC 60.375 63.158 17.22 4.95 0.00 2.87
758 1340 2.743718 CCTGACACGTGCCCTTCT 59.256 61.111 17.22 0.00 0.00 2.85
759 1341 2.358737 CCCTGACACGTGCCCTTC 60.359 66.667 17.22 6.17 0.00 3.46
760 1342 3.168528 ACCCTGACACGTGCCCTT 61.169 61.111 17.22 0.00 0.00 3.95
761 1343 3.626924 GACCCTGACACGTGCCCT 61.627 66.667 17.22 0.00 0.00 5.19
762 1344 4.699522 GGACCCTGACACGTGCCC 62.700 72.222 17.22 8.61 0.00 5.36
764 1346 2.424705 TTACGGACCCTGACACGTGC 62.425 60.000 17.22 9.30 40.12 5.34
765 1347 0.032403 TTTACGGACCCTGACACGTG 59.968 55.000 15.48 15.48 40.12 4.49
766 1348 0.752054 TTTTACGGACCCTGACACGT 59.248 50.000 0.00 0.00 42.71 4.49
767 1349 1.269936 ACTTTTACGGACCCTGACACG 60.270 52.381 0.00 0.00 0.00 4.49
768 1350 2.410939 GACTTTTACGGACCCTGACAC 58.589 52.381 0.00 0.00 0.00 3.67
769 1351 1.345415 GGACTTTTACGGACCCTGACA 59.655 52.381 0.00 0.00 0.00 3.58
770 1352 1.670967 CGGACTTTTACGGACCCTGAC 60.671 57.143 0.00 0.00 0.00 3.51
771 1353 0.604578 CGGACTTTTACGGACCCTGA 59.395 55.000 0.00 0.00 0.00 3.86
772 1354 0.319405 ACGGACTTTTACGGACCCTG 59.681 55.000 0.00 0.00 0.00 4.45
773 1355 0.605083 GACGGACTTTTACGGACCCT 59.395 55.000 0.00 0.00 0.00 4.34
774 1356 0.733909 CGACGGACTTTTACGGACCC 60.734 60.000 0.00 0.00 0.00 4.46
775 1357 0.240945 TCGACGGACTTTTACGGACC 59.759 55.000 0.00 0.00 0.00 4.46
776 1358 1.197721 TCTCGACGGACTTTTACGGAC 59.802 52.381 0.00 0.00 0.00 4.79
777 1359 1.466167 CTCTCGACGGACTTTTACGGA 59.534 52.381 0.00 0.00 0.00 4.69
778 1360 1.466167 TCTCTCGACGGACTTTTACGG 59.534 52.381 0.00 0.00 0.00 4.02
779 1361 2.771689 CTCTCTCGACGGACTTTTACG 58.228 52.381 0.00 0.00 0.00 3.18
780 1362 2.517935 GCTCTCTCGACGGACTTTTAC 58.482 52.381 0.00 0.00 0.00 2.01
781 1363 1.471684 GGCTCTCTCGACGGACTTTTA 59.528 52.381 0.00 0.00 0.00 1.52
782 1364 0.244178 GGCTCTCTCGACGGACTTTT 59.756 55.000 0.00 0.00 0.00 2.27
783 1365 1.596895 GGGCTCTCTCGACGGACTTT 61.597 60.000 0.00 0.00 0.00 2.66
784 1366 2.047443 GGGCTCTCTCGACGGACTT 61.047 63.158 0.00 0.00 0.00 3.01
785 1367 2.438795 GGGCTCTCTCGACGGACT 60.439 66.667 0.00 0.00 0.00 3.85
786 1368 3.878519 CGGGCTCTCTCGACGGAC 61.879 72.222 0.00 0.00 0.00 4.79
787 1369 4.405671 ACGGGCTCTCTCGACGGA 62.406 66.667 0.00 0.00 0.00 4.69
788 1370 4.180946 CACGGGCTCTCTCGACGG 62.181 72.222 0.00 0.00 0.00 4.79
789 1371 3.432588 ACACGGGCTCTCTCGACG 61.433 66.667 0.00 0.00 0.00 5.12
790 1372 2.179517 CACACGGGCTCTCTCGAC 59.820 66.667 0.00 0.00 0.00 4.20
791 1373 2.282251 ACACACGGGCTCTCTCGA 60.282 61.111 0.00 0.00 0.00 4.04
792 1374 1.583495 TACACACACGGGCTCTCTCG 61.583 60.000 0.00 0.00 0.00 4.04
793 1375 0.171455 CTACACACACGGGCTCTCTC 59.829 60.000 0.00 0.00 0.00 3.20
794 1376 0.539901 ACTACACACACGGGCTCTCT 60.540 55.000 0.00 0.00 0.00 3.10
795 1377 1.171308 TACTACACACACGGGCTCTC 58.829 55.000 0.00 0.00 0.00 3.20
796 1378 1.848652 ATACTACACACACGGGCTCT 58.151 50.000 0.00 0.00 0.00 4.09
797 1379 2.667473 AATACTACACACACGGGCTC 57.333 50.000 0.00 0.00 0.00 4.70
798 1380 3.243301 CGATAATACTACACACACGGGCT 60.243 47.826 0.00 0.00 0.00 5.19
799 1381 3.047796 CGATAATACTACACACACGGGC 58.952 50.000 0.00 0.00 0.00 6.13
800 1382 4.297299 ACGATAATACTACACACACGGG 57.703 45.455 0.00 0.00 0.00 5.28
801 1383 6.032094 AGAAACGATAATACTACACACACGG 58.968 40.000 0.00 0.00 0.00 4.94
802 1384 6.195983 GGAGAAACGATAATACTACACACACG 59.804 42.308 0.00 0.00 0.00 4.49
803 1385 6.474751 GGGAGAAACGATAATACTACACACAC 59.525 42.308 0.00 0.00 0.00 3.82
804 1386 6.406177 GGGGAGAAACGATAATACTACACACA 60.406 42.308 0.00 0.00 0.00 3.72
805 1387 5.981915 GGGGAGAAACGATAATACTACACAC 59.018 44.000 0.00 0.00 0.00 3.82
806 1388 5.069516 GGGGGAGAAACGATAATACTACACA 59.930 44.000 0.00 0.00 0.00 3.72
807 1389 5.069516 TGGGGGAGAAACGATAATACTACAC 59.930 44.000 0.00 0.00 0.00 2.90
808 1390 5.210430 TGGGGGAGAAACGATAATACTACA 58.790 41.667 0.00 0.00 0.00 2.74
809 1391 5.796424 TGGGGGAGAAACGATAATACTAC 57.204 43.478 0.00 0.00 0.00 2.73
810 1392 5.279809 GCATGGGGGAGAAACGATAATACTA 60.280 44.000 0.00 0.00 0.00 1.82
811 1393 4.505039 GCATGGGGGAGAAACGATAATACT 60.505 45.833 0.00 0.00 0.00 2.12
812 1394 3.751698 GCATGGGGGAGAAACGATAATAC 59.248 47.826 0.00 0.00 0.00 1.89
813 1395 3.392947 TGCATGGGGGAGAAACGATAATA 59.607 43.478 0.00 0.00 0.00 0.98
814 1396 2.174639 TGCATGGGGGAGAAACGATAAT 59.825 45.455 0.00 0.00 0.00 1.28
815 1397 1.562008 TGCATGGGGGAGAAACGATAA 59.438 47.619 0.00 0.00 0.00 1.75
816 1398 1.208706 TGCATGGGGGAGAAACGATA 58.791 50.000 0.00 0.00 0.00 2.92
817 1399 0.331278 TTGCATGGGGGAGAAACGAT 59.669 50.000 0.00 0.00 0.00 3.73
818 1400 0.111446 TTTGCATGGGGGAGAAACGA 59.889 50.000 0.00 0.00 0.00 3.85
819 1401 0.965439 TTTTGCATGGGGGAGAAACG 59.035 50.000 0.00 0.00 0.00 3.60
846 1428 3.628832 TCTGGGGAGAAATGGGTTTTT 57.371 42.857 0.00 0.00 0.00 1.94
847 1429 3.628832 TTCTGGGGAGAAATGGGTTTT 57.371 42.857 0.00 0.00 0.00 2.43
848 1430 3.852858 ATTCTGGGGAGAAATGGGTTT 57.147 42.857 0.00 0.00 0.00 3.27
849 1431 3.052869 GGTATTCTGGGGAGAAATGGGTT 60.053 47.826 0.00 0.00 0.00 4.11
850 1432 2.514160 GGTATTCTGGGGAGAAATGGGT 59.486 50.000 0.00 0.00 0.00 4.51
855 1437 2.488836 GAGGGGTATTCTGGGGAGAAA 58.511 52.381 0.00 0.00 0.00 2.52
942 1525 1.138266 TCGGGTCGGAATGGAGATTTC 59.862 52.381 0.00 0.00 0.00 2.17
946 1549 0.750850 GAATCGGGTCGGAATGGAGA 59.249 55.000 0.00 0.00 0.00 3.71
948 1551 0.978667 TGGAATCGGGTCGGAATGGA 60.979 55.000 0.00 0.00 0.00 3.41
952 1555 1.079681 CGTTGGAATCGGGTCGGAA 60.080 57.895 0.00 0.00 0.00 4.30
956 1559 2.165301 CGAGCGTTGGAATCGGGTC 61.165 63.158 0.00 0.00 32.93 4.46
973 1576 0.803768 CACTTGGATCGAGGAGTGCG 60.804 60.000 7.14 0.00 33.87 5.34
987 1590 1.808945 GTGGCCATGAGAGAACACTTG 59.191 52.381 9.72 0.00 0.00 3.16
989 1592 0.036952 CGTGGCCATGAGAGAACACT 60.037 55.000 21.08 0.00 0.00 3.55
990 1593 1.021390 CCGTGGCCATGAGAGAACAC 61.021 60.000 27.13 0.00 0.00 3.32
1005 1609 2.577112 CTACTCGCAGTCGCCGTG 60.577 66.667 0.00 0.00 35.26 4.94
1271 1931 4.586235 AGCCGGGCTTGCTGTTGT 62.586 61.111 17.69 0.00 33.89 3.32
1610 3189 1.209504 ACGAGCTAGCTAATTGGCCAA 59.790 47.619 23.00 23.00 0.00 4.52
1635 3214 0.318762 GTGGACGAAAGGCTCACTCT 59.681 55.000 0.00 0.00 40.87 3.24
1636 3215 0.318762 AGTGGACGAAAGGCTCACTC 59.681 55.000 0.00 0.00 44.00 3.51
1639 3224 0.318441 CAGAGTGGACGAAAGGCTCA 59.682 55.000 0.00 0.00 40.87 4.26
1640 3225 0.318762 ACAGAGTGGACGAAAGGCTC 59.681 55.000 0.00 0.00 40.87 4.70
1645 3254 1.412710 AGCAGAACAGAGTGGACGAAA 59.587 47.619 0.00 0.00 0.00 3.46
1653 3262 3.133003 AGTTGTACACAGCAGAACAGAGT 59.867 43.478 0.00 0.00 0.00 3.24
1659 3268 3.324846 AGATGGAGTTGTACACAGCAGAA 59.675 43.478 0.00 0.00 0.00 3.02
1678 3287 9.251440 CATGATTATCCATATCCAAAACCAGAT 57.749 33.333 0.00 0.00 0.00 2.90
1722 3349 4.262765 GGGACAGATCAGATGCATGTATCA 60.263 45.833 23.43 6.43 0.00 2.15
1723 3350 4.252073 GGGACAGATCAGATGCATGTATC 58.748 47.826 15.28 15.28 0.00 2.24
1840 3507 3.504520 GCTTATCCAAAACCGAAACAGGA 59.495 43.478 0.00 0.00 34.73 3.86
1889 3563 1.300931 GTGACAGGAGCAAGCGACA 60.301 57.895 0.00 0.00 0.00 4.35
1947 3621 1.270839 GCTCTGGTGCTCCAAGTTACA 60.271 52.381 9.14 0.00 43.81 2.41
1949 3623 1.055849 TGCTCTGGTGCTCCAAGTTA 58.944 50.000 9.14 1.80 43.81 2.24
1962 3646 1.871408 CGGAATCGAGGGATTGCTCTG 60.871 57.143 6.73 0.00 45.65 3.35
2007 3691 2.866923 TCACTGGGACTGGGATCATA 57.133 50.000 0.00 0.00 33.88 2.15
2012 3696 0.984230 GTTGATCACTGGGACTGGGA 59.016 55.000 0.00 0.00 45.53 4.37
2013 3697 0.391661 CGTTGATCACTGGGACTGGG 60.392 60.000 0.00 0.00 0.00 4.45
2015 3699 2.289072 ACTTCGTTGATCACTGGGACTG 60.289 50.000 0.00 0.00 0.00 3.51
2016 3700 1.971357 ACTTCGTTGATCACTGGGACT 59.029 47.619 0.00 0.00 0.00 3.85
2028 3712 0.868406 GGTTCAGCCTCACTTCGTTG 59.132 55.000 0.00 0.00 0.00 4.10
2031 3715 0.108615 ATCGGTTCAGCCTCACTTCG 60.109 55.000 0.00 0.00 34.25 3.79
2048 3738 3.494626 CAGTTCCACACACACAGTACATC 59.505 47.826 0.00 0.00 0.00 3.06
2053 3743 1.678728 CCACAGTTCCACACACACAGT 60.679 52.381 0.00 0.00 0.00 3.55
2054 3744 1.016627 CCACAGTTCCACACACACAG 58.983 55.000 0.00 0.00 0.00 3.66
2056 3746 1.873591 GATCCACAGTTCCACACACAC 59.126 52.381 0.00 0.00 0.00 3.82
2058 3748 1.523758 GGATCCACAGTTCCACACAC 58.476 55.000 6.95 0.00 32.79 3.82
2060 3750 0.034896 ACGGATCCACAGTTCCACAC 59.965 55.000 13.41 0.00 32.13 3.82
2062 3752 0.673644 CCACGGATCCACAGTTCCAC 60.674 60.000 13.41 0.00 32.13 4.02
2063 3753 1.125093 ACCACGGATCCACAGTTCCA 61.125 55.000 13.41 0.00 32.13 3.53
2064 3754 0.899720 TACCACGGATCCACAGTTCC 59.100 55.000 13.41 0.00 0.00 3.62
2065 3755 2.981859 ATACCACGGATCCACAGTTC 57.018 50.000 13.41 0.00 0.00 3.01
2066 3756 3.713826 AAATACCACGGATCCACAGTT 57.286 42.857 13.41 0.00 0.00 3.16
2067 3757 3.713826 AAAATACCACGGATCCACAGT 57.286 42.857 13.41 7.64 0.00 3.55
2068 3758 4.570772 CAGTAAAATACCACGGATCCACAG 59.429 45.833 13.41 1.13 0.00 3.66
2069 3759 4.020039 ACAGTAAAATACCACGGATCCACA 60.020 41.667 13.41 0.00 0.00 4.17
2071 3761 4.829872 ACAGTAAAATACCACGGATCCA 57.170 40.909 13.41 0.00 0.00 3.41
2072 3762 4.334481 CCAACAGTAAAATACCACGGATCC 59.666 45.833 0.00 0.00 0.00 3.36
2073 3763 4.201881 GCCAACAGTAAAATACCACGGATC 60.202 45.833 0.00 0.00 0.00 3.36
2074 3764 3.692593 GCCAACAGTAAAATACCACGGAT 59.307 43.478 0.00 0.00 0.00 4.18
2076 3766 2.159626 CGCCAACAGTAAAATACCACGG 60.160 50.000 0.00 0.00 0.00 4.94
2077 3767 2.726681 GCGCCAACAGTAAAATACCACG 60.727 50.000 0.00 0.00 0.00 4.94
2078 3768 2.414957 GGCGCCAACAGTAAAATACCAC 60.415 50.000 24.80 0.00 0.00 4.16
2079 3769 1.813786 GGCGCCAACAGTAAAATACCA 59.186 47.619 24.80 0.00 0.00 3.25
2080 3770 1.813786 TGGCGCCAACAGTAAAATACC 59.186 47.619 30.74 0.00 0.00 2.73
2099 3791 0.732880 CAACTGCTACGTCGTCCCTG 60.733 60.000 0.00 0.89 0.00 4.45
2101 3793 1.445582 CCAACTGCTACGTCGTCCC 60.446 63.158 0.00 0.00 0.00 4.46
2140 3833 6.405538 ACATCTTCATCTTCTTCCTCAAGTC 58.594 40.000 0.00 0.00 0.00 3.01
2222 3995 3.723835 CGTTCGTTCATCTAAAAAGGGCG 60.724 47.826 0.00 0.00 0.00 6.13
2292 4115 1.067516 GCAGCCAGTTTTGAGCAGAAA 59.932 47.619 0.00 0.00 0.00 2.52
2293 4116 0.670162 GCAGCCAGTTTTGAGCAGAA 59.330 50.000 0.00 0.00 0.00 3.02
2294 4117 0.179009 AGCAGCCAGTTTTGAGCAGA 60.179 50.000 0.00 0.00 0.00 4.26
2344 4242 1.302993 GGGTTTGGCTTGTCGGCTA 60.303 57.895 0.00 0.00 39.32 3.93
2470 4395 3.339141 GTTCCAGAGCTTCTACTTTGGG 58.661 50.000 1.74 0.00 41.25 4.12
2490 4415 4.099170 CTTCTCGGCCGTCGTCGT 62.099 66.667 27.15 0.00 40.32 4.34
2491 4416 4.831307 CCTTCTCGGCCGTCGTCG 62.831 72.222 27.15 10.89 40.32 5.12


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

AutoCloner maintained by Alex Coulton.